Re: [Freesurfer] -openmp flag in mri_em_register

[Harms, Michael]

The HCP Pipeline scripts use ‘bash’.  (setenv is for the csh shell).
The equivalent for bash is:

export OMP_NUM_THREADS=2

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Lisa Kramarenko 
mailto:lisa.kramare...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, June 8, 2017 at 9:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] -openmp flag in mri_em_register

Hi,
thanks for the quick reply. I pasted this line in the script, yet it gives me 
the following error:

setenv: command not found

Then I tried to just run it in the Terminal before calling the script, yet "No 
command 'setenv' was found".

Any idea on what is wrong?
Thanks,
Lisa

On 8 June 2017 at 15:26, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Lisa

the individual commands don't accept -openmp. Try doing:

setenv OMP_NUM_THREADS 2

mri_em_register ...

cheers
Bruce


On Thu, 8 Jun 2017, Lisa Kramarenko wrote:

Hello,
I am using HCP pipelines and I would like mri_em_register which is being
called from a pipeline script to run on 2 cores instead on all available
ones. I tried to just add an -openmp flag to the command as suggestedhere: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.
html

my command looks like this:

mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
"$SubjectDIR"/"$SubjectID"/mri/nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta -openmp 2


yet I get an error:

mri_em_register: could not open GCA -openmp

Do you have an idea of how to fix it?

Thanks!
Lisa


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Re: [Freesurfer] (no subject)

[Harms, Michael]

dcm2niix with the -s flag will allow you to convert a single DICOM that is
part of a directory with other DICOMs

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/7/17, 10:31 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anthony Dick"  wrote:

Hello Emily,

The easiest free way (that I know of) is using Osirix
(http://www.osirix-viewer.com/). In that program, there are a number of
export functions. You may want to view in that and export to DICOM. You
can then use dicom2nii
(http://people.cas.sc.edu/rorden/mricron/dcm2nii.html) to convert to a
single .nii file for input into Freesurfer. You may be able to skip the
Osirix step with what you have.

Anthony

On 6/7/17, 11:26 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Emily Rogers"  wrote:

Do you have any recommendations for programs to convert to a single
DICOM file? It seems that even using a single slice in the series is
causing errors and telling me the file does not exist even when it is in
the correct directory.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
Greve
Sent: Tuesday, June 06, 2017 5:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)

I did not mean for you to send them to me. You should use one of them
(any one of them) as input to  recon-all


On 06/06/2017 05:14 PM, Emily Rogers wrote:
> Yes I have the original 160 files, attached.
>
> Thanks for your help,
> Emily
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, June 06, 2017 5:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> I don't think we can read that. Do you have access to the orignal
dicoms?
>
>
> On 06/06/2017 04:58 PM, Emily Rogers wrote:
>> It was converted to a single dicom from individual slice files
using MIPAV image viewer. It is a single subject structural MRI.
>>
>>
https://urldefense.proofpoint.com/v2/url?u=http-3A__www69.zippyshare.com_v_
MJDVstW0_file.html&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrj
wA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=ocZR0DZOeaCCHg4-JY0dFyPk
byXnSqvxQR2FSAqmqYA&e=
>> I've uploaded it here
>>
>> Thanks,
>> Emily
>>
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, June 06, 2017 4:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] (no subject)
>>
>> mri_convert is having a problem reading 1400composite.dcm. It is not
>> even recognizing it as a dicom. Where did it come from and what is
in it?
>>
>>
>> On 06/06/2017 04:35 PM, Emily Rogers wrote:
>>> Apologies-- This email contains attachment. Thank you.
>>>
>>> 
>>>
>>> Hello,
>>>
>>> I am trying to implement using Freesurfer segmentation in my
analysis for MEG data. I am trying to segment this structural MRI
(1400composite.dcm) and I keep getting errors. I have attached the log
file. Any help is appreciated.
>>>
>>> Thank you,
>>> Emily
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e
du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC
JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6
WiILFEaa8IiBASTirJieum__uLBqgU4&e=
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop:
https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.e
du_filedrop2&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrjwA&m=g
4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=p-SDsa3-uDTqXPjqOoKITKQHFEBRxv
ADzktTFw_0Rcs&e=
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.e
du_transfer_outgoing_flat_greve_&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWj
wCJRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=UqaC

Re: [Freesurfer] Ghosting Artifact

[Harms, Michael]

That subjects looks like a candidate for exclusion, because the SNR anteriorly 
is much less than posteriorly.  It looks to me like there is either a problem 
with your head coil, or the anterior coil elements were not active.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Fotiadis, Panagiotis" 
mailto:pfotia...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, January 27, 2017 at 12:30 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Ghosting Artifact

Hello,

I have a T1 weighted scan with a semi-severe ghosting artifact, and recon-all 
is not able to complete the reconstruction process (according to recon-all log, 
it tries to fix 237 defects and at defect 209 the recon stops).
Is there anything that I can do to recover the scan so I can reconstruct it 
successfully? (I have attached a few pics indicating the artifact).

Thanks in advance for your time!

Best,
Panos

Panagiotis Fotiadis
Research Technologist II
J. P. Kistler Stroke Research Center
Massachusetts General Hospital
175 Cambridge Street, Suite 300
Boston, MA, 02114
T: (617) 643-3869


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Re: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads

[Harms, Michael]

Wow, that’s a terrible correlation between two putative measures of head size.

What does the scatterplot of FS’s “eTIV” vs “SupraTentorialVol” look like?  The 
latter is based on the surfaces, so a scatterplot of the two can be a good way 
to identify cases where the talairach.xfm file (from which “eTIV” is derived) 
isn’t very accurate.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Jeffrey Crawford mailto:jcraw...@jhmi.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, December 16, 2016 at 11:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads

Hello everyone!

I have some questions about FS eTICV.
I read on the Wiki that eTICV is not the best measure of ICV and saw the same 
from other articles. The alternative I decided on was measuring the TICV using 
CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV 
from CAT12 to see how they match each other on measurment. FS is the variable 
on the Y-axis and CAT12 is the variable on the X-axis. If we assume that CAT12 
is more accurate than FS, then it looks as though the FS begins to become more 
inaccurate as the head size gets smaller.

[cid:image001.png@01D2579B.8A615E30]

So here are my questions:

1.  Is my interpretation of this scatterplot correct?

2.  Does FS generally have more difficulty measuring smaller heads? If so, 
then why?

3.  Is it more advised for me to use the CAT12 TICV measure as a covariate 
in my future analysis? Or maybe some other program that I don’t know about?





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Re: [Freesurfer] DTI Multi band sequence?

[Harms, Michael]

That would be yet another way.
For those that are curious, the field is “MosaicRefAcqTimes”.

cheers,
-MH
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 11/30/16, 11:16 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of dgw"  wrote:

I can't remember the tag numbers, but I believe the time of slice
acquisition is in the dicom. You should be able to just pull that
field on one volume and compare the field for all slices and see if
any of them have the same time.

hth
d

On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja  wrote:
> Hi,
>
> I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
> whether the DTI data (in DICOM format) I have is multi-band sequence?
>
> I used dicominfo in MATLAB but couldn't find any information related to
> multi-band in the dicom header.
>
> Any help would be really appreciated.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
>it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] DTI Multi band sequence?

[Harms, Michael]

Hi Martin,
I’ve addressed this in your query to the FSL list.  Please see my response 
there.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Martin Juneja mailto:mj70...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, November 30, 2016 at 11:10 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] DTI Multi band sequence?

Hi,

I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine 
whether the DTI data (in DICOM format) I have is multi-band sequence?

I used dicominfo in MATLAB but couldn't find any information related to 
multi-band in the dicom header.

Any help would be really appreciated.


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Re: [Freesurfer] Longitudinal Stream on HCP Data

[Harms, Michael]

To clarify, in that post, Matt wasn’t saying that FS was going to incorporate 
myelin maps.  Rather, the new (v6) version of FS, with its support of data 
acquired with < 1 mm resolution, may eliminate the need for some of the steps 
that are currently the HCP Pipelines that are there to take full advantage of 
higher resolution structural acquisitions.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, November 8, 2016 at 9:15 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Longitudinal Stream on HCP Data

Hi Freesurfer/HCP experts,

I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into 
the FreeSurfer processing stream.
Matthew Glasser mentioned in a post on the HCP mailing list about a month back 
that this is being actively worked on by FreeSurfer: 
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html.
Are there any workflows or development versions that I can download in order to 
perform something like this.

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)


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Re: [Freesurfer] Recon-all Exiting without Error

[Harms, Michael]

Hi,
Is this just an exercise to try to duplicate the HCP processing? Because we’ve 
already run all subjects (with released structural data) through FreeSurfer for 
users.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Natalie Busby 
mailto:natalie.bu...@manchester.ac.uk>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, October 31, 2016 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all Exiting without Error

Hi,

I have just started using FreeSurfer and I am trying to do the subcortical 
segmentation on some Human Connectome Data.

In the command line I typed,
‘recon-all –i T1w_acpc_dc_restore_1.25.nii –subjid 100307’

The following output was produced:

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/100306

mri_convert 
/home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii 
/usr/local/freesurfer/subjects/100306/mri/orig/001.mgz

mri_convert 
/home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii 
/usr/local/freesurfer/subjects/100306/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii...
TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz...

#--

Started at Mon Oct 31 10:12:26 EDT 2016
Ended   at Mon Oct 31 10:12:31 EDT 2016
#@#%# recon-all-run-time-hours 0.001
recon-all -s 100306 finished without error at Mon Oct 31 10:12:31 EDT 2016
done

I was wondering if you knew what the problem was?

Thank you!

Best wishes,

Natalie



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Re: [Freesurfer] TRACULA longitudinal stream: using multiple configuration files?

[Harms, Michael]

Hi,
I remember looking into this — all the time points for a given subject need to 
be specified in the same configuration file, otherwise you don’t get the 
longitudinal aspect of the processing.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
"j.oschw...@psychologie.uzh.ch" 
mailto:j.oschw...@psychologie.uzh.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, October 25, 2016 at 2:29 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA longitudinal stream: using multiple configuration 
files?

Hi Freesurfer users

I wonder wether it makes a difference when using longitudinal TRACULA if all 
timepoints are run within one process (1 configuration file including all three 
timepoints) or if it is possible to split it into several independent processes 
(with several different configuration files - one per time point)?

Thank you for your help.
Jessica


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Re: [Freesurfer] Cortical thickness using qdec (between scanners)

[Harms, Michael]

Hi,
Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect.  In my opinion, this falls into the “not possible at all” category.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Martin Juneja 
Reply-To: Freesurfer support list 
Date: Thursday, September 29, 2016 at 1:54 PM
To: Freesurfer support list 
Subject: [Freesurfer] Cortical thickness using qdec (between scanners)





Hello FS experts,


I have a data set of 20 subjects (patients) collected at location-1 with 3T Siemens scanner. Also, I have a set of age-matched 20 subjects (controls) collected at location-2 with 3T Siemens scanner.


I am interested in comparing cortical thickness between controls and patients using FreeSurfer but I am not sure if I can do that since I have both the data sets collected at two different locations.


I would really appreciate any inputs on this.


I tried to find some papers on scanner differences but all I could find was between 1.5 T vs 3T or 3T vs 7T. Is there any special covariates I need to define for this purpose (if so then at which step during analysis?) or is it not possible at all?


Thanks.






 



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Re: [Freesurfer] Multi-band slice timing correction

[Harms, Michael]

Hi,
One comment:  I don’t know about the details of these particular scripts,
but users should be aware that different SMS/MB implementations (e.g.,
CMRR vs. Siemens/MGH) do not necessarily use the same slice ordering.  The
safest thing to do is confirm the timing from the DICOMs.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 9/7/16, 4:55 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"  wrote:



On 09/01/2016 04:31 PM, Wang, Ruosi wrote:
> Dear Freesurfer developers:
>
> I'm seeking out ways for performing multi-band slice timing correction
> with freesurfer 5.3. I've searched the mailing list, and noticed that
> there might be a couple of ways for doing this. But, I still have some
> conerns for different ways, and please see below for my questions:
>
> 1) using new version of stc.fsl and slicedelay
>
> I tried to download these files from a link provided in an emai loop
>
>l> of
> the mailing archive, but failed to do so. Could you please share the
> updated downloading link to these files. In addition, what kinds of
> information shall I provide?  The slice order and number of SMS slice
> groups?
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fsl
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/slicedelay
>
>
Try now
> 2) using freesurfer 6 for preprocessing
> Since freesurfer 6 is still in beta version, can I use the
> proproc-sess of fs6 for data preprocessing only and switch to fs 5.3
> afterwards for all the other anlaysis? Is there any downside for this,
> in comparison with just using the new version of stc.fsl and sliceday?
I would be careful using fs6 for anything you don't want to have to redo.
> In addition, for the input file so of -sliceorder, shall it be the
> slice number ordered by time? And for the input file of -ngroups,
> shall it be the number of slices that are colloected at the same time?
The slice order is up, down, siemens, etc. The number of groups is the
number of slices acquired simultaneously
> Thank you so much, it is deeply appreciated.
> Best,
> Ruosi
> --
> Ruosi Wang
> Graduate Student Vision Lab in Psychology Department
> Harvard University
> William James Hall, 7 floor
> 33 Kirkland Street
> Cambridge, MA 02138
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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e-mail
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properly
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Harms, Michael]

FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of "Krieger, Donald N." 
Reply-To: 'Freesurfer support list' 
Date: Tuesday, August 30, 2016 at 9:25 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run








Thank you – very helpful.
 

Best – Don

 



From:
freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
On Behalf Of Douglas Greve
Sent: Tuesday, August 30, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run


 
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
 

On 8/30/16 10:12 AM, Krieger, Donald N. wrote:


Dear list:
 
What are the advantages of including a T2 scan when running recon-all –all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
 
Thanks and best - Don
 




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Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Harms, Michael]

Sure, any simulation can’t be exhaustive, but my understanding, chatting
with Anderson, is that their 2014 paper simulated a quite large space of
designs and Freedman-Lane is appropriate for the vast majority of the GLMs
that we would encounter in neuroimaging.

Also, again per Anderson, I believe that method implemented in
mri_glmfit-sim is that of Manly for those interested in linking what
mri_glmfit-sim is doing to the results in Winkler (e.g., Table 7).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/30/16, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas Greve"  wrote:

By "wrong" I meant that permutation no longer  gives exact p-values in
expectation with non-orthogonal designs. There is no theory to
characterize the accuracy of  Freeman-Lane of the other methods. In this
sense, they are not approximations but ad hoc methods that people hope
do a better job than parametric methods. Anderson tested them on a wide
range of designs, but it was, of course, not exhaustive. The accuracy of
his results may not extend to other designs, so it is a buyer-beware
situation (as with all neuroimaging).


On 8/29/16 10:16 PM, Harms, Michael wrote:
> Hi,
> I wouldn’t say that non-orthogonal designs are “wrong” to use with
> permutation.  Rather, there are different approaches to handling that
> situation and produce approximate p-values.  See Table 2 in Winkler’s
>2014
> paper, and the results therein comparing the various approaches:
>
> http://www.ncbi.nlm.nih.gov/pubmed/24530839
>
>
> PALM actually gives you control over the method used, with the default
> (and recommended) approach being that of “Freedman-Lane", which is the
> same approach used by FSL’s ‘randomise’ tool to handle correlated
> covariates.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Matt Glasser"  m...@ma-tea.com> wrote:
>
> PALM handles GIFTI and CIFTI data.
>
> Peace,
>
> Matt.
>
> On 8/29/16, 6:21 PM, "Douglas N Greve"
>  gr...@nmr.mgh.harvard.edu> wrote:
>
>> Does PALM do surface-based? Also, there is no way to appropriately
>> handle this. For permutation, non-orthogonal designs are wrong. There
>> are ways to try to compensate for it, which is what PALM is doing. Sorry
>> to be nit-picky!
>>
>>
>> On 08/29/2016 06:12 PM, Harms, Michael wrote:
>>> Hi Maaike,
>>> Why not just use PALM?  Then you don¹t have to worry about this (since
>>> PALM appropriately handles the situation of correlated covariates).
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>>
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>>
>>>
>>>
>>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>> of
>>> Douglas N Greve" >> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>> It is hard to say. Since the subjects are not exchangeable, the
>>> permutation is technically not appropriate. Check the winkler paper,  I
>>> think he talks about what happens if you just don't do anything.
>>>
>>>
>>> On 08/29/2016 11:07 AM, maaike rive wrote:
>>>> Hi all,
>>>>
>>>>
>>>> Is using forced permutation for non-orthogonal design matrices wrong
>>>> or is it allowed to do this instead of using tools like palm (what
>>>> happens eg with the covariates when using forced permutation)? I
>>>> used forced permutation  and it seemed to work, results were (partly)
>>>> comparable to what I found with monte carlo simulations.
>>>>
>>>>
>>>> Thanks, Maaike
>>>>
>>>>
>>>>
>>>>

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Harms, Michael]

Hi,
I wouldn’t say that non-orthogonal designs are “wrong” to use with
permutation.  Rather, there are different approaches to handling that
situation and produce approximate p-values.  See Table 2 in Winkler’s 2014
paper, and the results therein comparing the various approaches:

http://www.ncbi.nlm.nih.gov/pubmed/24530839


PALM actually gives you control over the method used, with the default
(and recommended) approach being that of “Freedman-Lane", which is the
same approach used by FSL’s ‘randomise’ tool to handle correlated
covariates.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Matt Glasser"  wrote:

PALM handles GIFTI and CIFTI data.

Peace,

Matt.

On 8/29/16, 6:21 PM, "Douglas N Greve"
 wrote:

>Does PALM do surface-based? Also, there is no way to appropriately
>handle this. For permutation, non-orthogonal designs are wrong. There
>are ways to try to compensate for it, which is what PALM is doing. Sorry
>to be nit-picky!
>
>
>On 08/29/2016 06:12 PM, Harms, Michael wrote:
>> Hi Maaike,
>> Why not just use PALM?  Then you don¹t have to worry about this (since
>> PALM appropriately handles the situation of correlated covariates).
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Douglas N Greve" > gr...@nmr.mgh.harvard.edu> wrote:
>>
>> It is hard to say. Since the subjects are not exchangeable, the
>> permutation is technically not appropriate. Check the winkler paper,  I
>> think he talks about what happens if you just don't do anything.
>>
>>
>> On 08/29/2016 11:07 AM, maaike rive wrote:
>>> Hi all,
>>>
>>>
>>> Is using forced permutation for non-orthogonal design matrices wrong
>>> or is it allowed to do this instead of using tools like palm (what
>>> happens eg with the covariates when using forced permutation)? I
>>> used forced permutation  and it seemed to work, results were (partly)
>>> comparable to what I found with monte carlo simulations.
>>>
>>>
>>> Thanks, Maaike
>>>
>>>
>>>
>>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  namens Harms, Michael
>>> 
>>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
>>> *Aan:* Freesurfer support list
>>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
>>> running after 3 days!
>>>
>>> Hi,
>>> You might want to check out FSL¹s PALM tool, which has a bit more
>>> sophisticated permutation framework, and allows for permutation in the
>>> context of non-orthogonal covariates.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>> From: >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay
>>> Kurani mailto:dr.ajay.kur...@gmail.com>>
>>> Reply-To: Freesurfer support list >> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Date: Thursday, August 25, 2016 at 4:13 PM
>>> To: Freesurfer support list >> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
>>> after 3 days!
>>>
>>> Hi Doug,
>>> Thanks for the help!  I think I figured out the issue based on your
>>> response.
>>> 1) I created a template to use for this group and named it fsaverage
>>> (including creating monte carlo simulations) for simp

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Harms, Michael]

Hi Maaike,
Why not just use PALM?  Then you don’t have to worry about this (since
PALM appropriately handles the situation of correlated covariates).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"  wrote:

It is hard to say. Since the subjects are not exchangeable, the
permutation is technically not appropriate. Check the winkler paper,  I
think he talks about what happens if you just don't do anything.


On 08/29/2016 11:07 AM, maaike rive wrote:
>
> Hi all,
>
>
> Is using forced permutation for non-orthogonal design matrices wrong
> or is it allowed to do this instead of using tools like palm (what
> happens eg with the covariates when using forced permutation)? I
> used forced permutation  and it seemed to work, results were (partly)
> comparable to what I found with monte carlo simulations.
>
>
> Thanks, Maaike
>
> 
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>  namens Harms, Michael
> 
> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
> *Aan:* Freesurfer support list
> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
> running after 3 days!
>
> Hi,
> You might want to check out FSL’s PALM tool, which has a bit more
> sophisticated permutation framework, and allows for permutation in the
> context of non-orthogonal covariates.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay
> Kurani mailto:dr.ajay.kur...@gmail.com>>
> Reply-To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, August 25, 2016 at 4:13 PM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
> after 3 days!
>
> Hi Doug,
>Thanks for the help!  I think I figured out the issue based on your
> response.
> 1) I created a template to use for this group and named it fsaverage
> (including creating monte carlo simulations) for simplicity of
> integrating with freesurfer as I am newer to it.  This is why the
> sizes didn't match up as you expected
> but the mri_glmfit still ran.
>
> 2) I deleted the folder and restarted without background processes.
> The error became apparent.  Of my covariates (2 fix factors and 3
> quantitative), not all were orthogonal.  In looking at the error more,
> it seems that i need to add the
> --perm-force if I wanted the simulation to run, however the background
> processes were not aware of this error and kept polling as you mentioned.
>
> This brings me to a new but related issue.  From what I have read in
> other freesurfer posts, it is statistically incorrect to use
> --perm-force for non-orthogonal covariates (or continuous covariates).
> I am unsure how to proceed.
> a) If I ran permutation testing (to overcome the issue of incorrect
> smoothness estimations from the gaussian distribution assumption),
> then I run into the issue of non-orthogonal covariates.  Is there a
> way to orthogonalize the data in
> freesurfer, or a solution to this issue?
>
> b) If orthogonalizing is difficult to implement, another option is
> running Qdec with the montecarlo simulation at a more conservative p
> value (p< 0.001).  From your previous posts, the testing at this p
> value for 10mm seems to meet the 5% FPR.  One question is if the
> non-orthogonal data affects this analysis as well for this model?
>
> Thanks,
> Ajay
>
> On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani
> mailto:dr.ajay.kur...@gmail.com>> wrote:
>
> Hi Freesurfer Experts,
>I am trying to use freesurfer's mri_glmfit-sim tool to run
> permutation testing on cortical thickness data (as recommended by
> Doug in my previous post:
>
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html
>
><http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.htm
>l>
> )
>
> Most of the tutorials I found were not related to per

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Harms, Michael]

Hi,
You might want to check out FSL’s PALM tool, which has a bit more sophisticated permutation framework, and allows for permutation in the context of non-orthogonal covariates.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Ajay Kurani 
Reply-To: Freesurfer support list 
Date: Thursday, August 25, 2016 at 4:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!








Hi Doug,

   Thanks for the help!  I think I figured out the issue based on your response. 


1) I created a template to use for this group and named it fsaverage (including creating monte carlo simulations) for simplicity of integrating with freesurfer as I am newer to it.  This is why the sizes didn't match up as you expected

    but the mri_glmfit still ran.  


2) I deleted the folder and restarted without background processes.  The error became apparent.  Of my covariates (2 fix factors and 3 quantitative), not all were orthogonal.  In looking at the error more, it seems that i need to add the

--perm-force if I wanted the simulation to run, however the background processes were not aware of this error and kept polling as you mentioned.



This brings me to a new but related issue.  From what I have read in other freesurfer posts, it is statistically incorrect to use --perm-force for non-orthogonal covariates (or continuous covariates).  I am unsure how to proceed.
a) If I ran permutation testing (to overcome the issue of incorrect smoothness estimations from the gaussian distribution assumption), then I run into the issue of non-orthogonal covariates.  Is there a way to orthogonalize the data in

    freesurfer, or a solution to this issue?


b) If orthogonalizing is difficult to implement, another option is running Qdec with the montecarlo simulation at a more conservative p value (p< 0.001).  From your previous posts, the testing at this p value for 10mm seems to meet the 5% FPR.  One question
 is if the non-orthogonal data affects this analysis as well for this model?


Thanks,

Ajay



On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani 
 wrote:





Hi Freesurfer Experts,

   I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html )

Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect.  Please let me know where I go wrong...

1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim.  I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing.  The following is for just the
 left hemisphere.   Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 



2) I ran the following command:
/mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 2 perm.abs.2 --sim-sign abs --bg 16

Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails).  I assumed that by removing this estimate, it would force the permutation test to calculate based on the
 data but when looking at the log output I see the following which says fwhm 0:

cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx
 --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh
 --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013



3)I started this a few days ago on a 16 core machine and it is still running in the terminal.  I have 150 subjects in the analysis and specified 1 iterations.  In the terminal I assumed when I reach Poll 1 

Re: [Freesurfer] TRACULA: narrow probability distributions

[Harms, Michael]

Ok.  We’ll give it a try.  Just to confirm, you're agreeing that
increasing nburnin and nsample is a “good” thing, right?  (e.g., 1000, and
15000, respectively?)  If anything, we should be less likely to get narrow
tracts when using larger nburnin/nsample values, right?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/23/16, 5:09 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Michael - Even if it starts very close to the true max of the
distribution, in practice it'll never stay put. MCMC will accept a new
sample path with probability 1 if the new sample has greater probability
than the previous sample, and it will also accept it with some very small
probability if it doesn't. This means that it'll still explore the space
around the max, even if it ends up returning to the max pretty quickly. So
most likely there's something weird about the initial path if it doesn't
move at all.

Best,

a.y

On Tue, 23 Aug 2016, Harms, Michael wrote:

>
> Hi Anastasia,
> My interpretation of the “reinit” parameter is that it is for situations
> where a narrow probability distribution is assumed to be incorrect.  But
> how do you know whether it is indeed incorrect, or whether in fact the
> true equilibrium distribution is (correctly) very narrow?
>
> In particular, my understanding of MCMC is that higher burn-in, and more
> sampling iterations are only a “good” thing.  i.e., If we have the time
> and compute resources, we shouldn’t hesitate to increase them from their
> defaults, to help to make sure we are capturing the true equilibrium
> distribution.  So, if increasing the nburnin and nsample values makes it
> more likely to find spatially narrow tract distributions, isn’t that a
> sign that the true distribution should indeed be narrow?
>
> thanks,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Anastasia Yendiki"  ayend...@nmr.mgh.harvard.edu> wrote:
>
>
> Hi Dillan - There's a work-around for this, see the reinit variable at
>the
> bottom of the sample config file:
> http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
>
> I'm hoping to make this happen automatically soon!
>
> Best,
>
> a.y
>
> On Tue, 23 Aug 2016, Newbold, Dillan wrote:
>
>> Dear Anastasia,
>>
>> I’ve been looking at a lot of Tracula path.pd files and I’ve found that
>> some probability distributions are only a single voxel wide, similar to
>> the path.map file. The few none-zero voxels in these path.pd files have
>> very high probability values. When an isosurface is generated for these
>> tracts, it looks like a short thin blob somewhere in the usual tract
>> distribution. I’ve seen descriptions in the archives of similar “short
>> thin tracts,” but, from what I have seen, no one has offered a
>>satisfying
>> explanation for why these occur.
>>
>> What I think is happening in these tracts is that a maximum-probability
>> (or local maximum) path is found during a burn-in iteration and all
>> following perturbations of that path are rejected. Since the probability
>> value in the path.pd is equal to the number of sample paths intersecting
>> that voxel, finding a local maximum early on results in a small number
>>of
>> very high-probability voxels. Consistent with this explanation, I’ve
>> found that this issue occurs more frequently when nburnin is set to 1000
>> (default = 200). A similar issue can occur if a local maximum is found
>> early during the sample iterations, and this results in a path.pd file
>> containing a small number of voxels with very high values surrounded by
>>a
>> larger area of low-value voxels. When a 20% threshold is applied, the
>> result is the same as when a local maximum occurs during a burn-in
>> iteration.
>>
>> Does my understanding of this issue seem correct?
>>
>> None of this would be a problem if my only aim were to find the single
>> path with the maximum a posteriori probability, but I’m concerned that
>> the average and weighted_average sats for these 

Re: [Freesurfer] TRACULA: narrow probability distributions

[Harms, Michael]

Hi Anastasia,
My interpretation of the “reinit” parameter is that it is for situations
where a narrow probability distribution is assumed to be incorrect.  But
how do you know whether it is indeed incorrect, or whether in fact the
true equilibrium distribution is (correctly) very narrow?

In particular, my understanding of MCMC is that higher burn-in, and more
sampling iterations are only a “good” thing.  i.e., If we have the time
and compute resources, we shouldn’t hesitate to increase them from their
defaults, to help to make sure we are capturing the true equilibrium
distribution.  So, if increasing the nburnin and nsample values makes it
more likely to find spatially narrow tract distributions, isn’t that a
sign that the true distribution should indeed be narrow?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Dillan - There's a work-around for this, see the reinit variable at the
bottom of the sample config file:
 http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

I'm hoping to make this happen automatically soon!

Best,

a.y

On Tue, 23 Aug 2016, Newbold, Dillan wrote:

> Dear Anastasia,
>
> I’ve been looking at a lot of Tracula path.pd files and I’ve found that
>some probability distributions are only a single voxel wide, similar to
>the path.map file. The few none-zero voxels in these path.pd files have
>very high probability values. When an isosurface is generated for these
>tracts, it looks like a short thin blob somewhere in the usual tract
>distribution. I’ve seen descriptions in the archives of similar “short
>thin tracts,” but, from what I have seen, no one has offered a satisfying
>explanation for why these occur.
>
> What I think is happening in these tracts is that a maximum-probability
>(or local maximum) path is found during a burn-in iteration and all
>following perturbations of that path are rejected. Since the probability
>value in the path.pd is equal to the number of sample paths intersecting
>that voxel, finding a local maximum early on results in a small number of
>very high-probability voxels. Consistent with this explanation, I’ve
>found that this issue occurs more frequently when nburnin is set to 1000
>(default = 200). A similar issue can occur if a local maximum is found
>early during the sample iterations, and this results in a path.pd file
>containing a small number of voxels with very high values surrounded by a
>larger area of low-value voxels. When a 20% threshold is applied, the
>result is the same as when a local maximum occurs during a burn-in
>iteration.
>
> Does my understanding of this issue seem correct?
>
> None of this would be a problem if my only aim were to find the single
>path with the maximum a posteriori probability, but I’m concerned that
>the average and weighted_average sats for these tracts will be less
>accurate. Since these distributions include small fractions of the number
>of voxels included in most tract distributions, is it likely that the
>average and weighted_average stats from these narrow distributions are
>less representative of the whole tract and more subject to random noise?
>
> Given these concerns, what type of overall path statistics do you think
>is most descriptive of a tract? Also, do you feel that higher nburnin and
>nsample values should lead to superior results? I would have thought this
>to be the case, but now it seems to me that setting either of these
>values too high will result in narrow probability distributions and bad
>statistics.
>
> Thank you,
> Dillan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>



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Re: [Freesurfer] FSFAST ROI atlas

[Harms, Michael]

Yes, the Gordon parcellation paper:

http://www.ncbi.nlm.nih.gov/pubmed/25316338





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sabin Khadka <mr.sabinkha...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 18, 2016 at 8:55 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael 
<mha...@wustl.edu> wrote:





They are attached (assuming that the FS list allows small attachments).
There is a script that details exactly how it was done.





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Sabin Khadka <mr.sabinkha...@gmail.com>
Date: Wednesday, August 17, 2016 at 11:25 AM
To: Freesurfer support list <freesur...@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>


Subject: Re: [Freesurfer] FSFAST ROI atlas









Hi Michael- Is there anyway I can get those Gordon parcellation annot files?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael 
<mha...@wustl.edu> wrote:






FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:



Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!





Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu> wrote:



I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:








HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 



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Re: [Freesurfer] FSFAST ROI atlas

[Harms, Michael]

FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From:  on behalf of Doug Greve 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:


Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!




Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
 wrote:


I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:







HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 


___
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 please contact the Partners Compliance HelpLine at 
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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA: 20% default threshold

[Harms, Michael]

Thanks for clarifying.  Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?

thx,
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Dillan - Thank you for your support!

Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.

Best,

a.y

On Tue, 26 Jul 2016, Newbold, Dillan wrote:

> Hi everyone,
>
> I’m having a little trouble understanding the exact meaning of the 20%
>default threshold used in the freeview -tv option and dmri_pathstats
>--pthr. I’ve seen multiple threads where Anastasia said that it is 20% of
>the maximum value in the probability distribution—which corresponds to
>the maximum number of sample paths intersecting a single voxel—but the
>default thresholds I’ve seen set by the -tv option are generally lower
>than that. For example, I have one subject in whom the right CST has a
>maximum value in its path.pd.nii.gz file of 300. I would expect based on
>what I’ve read in the mail archives that the threshold would be set at
>60, but when I open the merged file with the -tv option the default
>threshold for the right CST is 35.
>
> My current best guess is that the default threshold is set to produce a
>volume that has a probability sum equal to 20% of the sum of the
>pre-threshold volume. (That is, the sum of intensities of all voxels in
>the path.pd.nii.gz file should be 5 times the sum of the voxels above the
>default threshold.) Is that accurate?
>
> Thanks for all you’ve done to develop this tool. It’s brilliant and I
>want to understand as much of it as I can.
>
> -Dillan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>



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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Harms, Michael]

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

From the last post in that thread, it is unclear if the issue was ever
resolved.  Was it resolved off the list?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/26/16, 11:22 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Michael - Which build of freesurfer do you use? I can send you the new
version of dmri_paths so you can try it out.

Best,

a.y

On Wed, 20 Jul 2016, Harms, Michael wrote:

>
> Hi Anastasia,
>
> I was wondering what the resolution to this thread was:
>
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html
>
> It sounds like a new version of dmri_paths was deemed necessary to
> appropriately process single time points in the longitudinal TRACULA
>stream,
> but Janosch’s last post seemed to indicate that her issue wasn’t resolved
> even with the new build of dmri_paths that you generated.
>
> thanks,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
>
>
>
>
>__
>__
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the
>contents
> of this information is strictly prohibited. If you have received this
>email
> in error, please immediately notify the sender via telephone or return
>mail.
>
>



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Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Harms, Michael]

Hi,
Bumping this up for AY.  


We have a bunch of jobs we want to send to our cluster, and we are wondering if we need a revised version of dmri_paths to properly handle single time points in the TRACULA longitudinal stream.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mha...@wustl.edu>
Reply-To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 20, 2016 at 11:59 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Cc: Dillan Newbold <newb...@wustl.edu>
Subject: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream









Hi Anastasia,


I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html


It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal TRACULA stream, but Janosch’s last post seemed to indicate that her issue wasn’t resolved even with the new build of dmri_paths
 that you generated.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.





 



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[Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Harms, Michael]

Hi Anastasia,


I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html


It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal TRACULA stream, but Janosch’s last post seemed to indicate that her issue wasn’t resolved even with the new build of dmri_paths
 that you generated.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






 



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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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Re: [Freesurfer] question about white matter edits

[Harms, Michael]

Hi,
The missing sulcus may be a consequence of the topology correction going awry.  Check the “nofix” surface to see the surface before topology correction.  If the topology correction is the problem, you’ll need to edit the wm.mgz.  There is an example on
 the FS tutorials.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From:  on behalf of Barbara Kreilkamp 
Reply-To: Freesurfer support list 
Date: Wednesday, July 6, 2016 at 12:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about white matter edits





Hi Rito,
I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel
 value less than 110)." from 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview

Could it be that those control points grasp voxels that already have an intensity of at least 110? 
Best wishes,
Barbara





On 06/07/2016 17:25, Ritobrato Datta wrote:


Hi All,

We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid 

but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack



 
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Re: [Freesurfer] segmentation issues in Temporal Lobes

[Harms, Michael]

Hi,
There is nothing to solve — that is the expected behavior around the
hippocampus/amygdala.

See this FAQ:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac
esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt
hestructuresthere.HowcanIfixthis.3F

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/6/16, 4:47 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Barbara Kreilkamp"  wrote:

Dear Freesurfers,

Unfortunately I am having a problem with recon-all segmentation in some
of my participants.

It seems that part of the brain is cut off in the medial part of the
Temporal lobes (please see attachment), around the region where the
hippocampus is.

I am unable to place WM region control points, as the algorithm does not
have seemed to miss white matter, rather only gray matter of the
hippocampus.

I've seen on your website that also there the cortical surface does not
include the hippocampus, so I wonder if this is intentional? Problem is
that the surface here grasps some of the hippocampus but not all of it.

What is the best way of solving this?

Thanks very much.

Best wishes,

Barbara




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Re: [Freesurfer] controlling for total gray matter volume

[Harms, Michael]

Hi,
Why not use total surface area to control for analyses involving area, and
mean cortical thickness to control for thickness?  I’ve posted to the list
before regarding this, so you should be able to find those posts.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/4/16, 9:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Clara Kühn"  wrote:

Do you know, if there are any publications concerning this matter? So far
I've found only this
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852
that controls for tGM only for area and not CT.

Cheers Clara

- Ursprüngliche Mail -
Von: "Bruce Fischl" 
An: "Freesurfer support list" 
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume

sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:

> I have decided now to not control for ICV or total gray matter volume
>when looking at cortical thickness but to control for total gray matter
>volume when looking at surface area. Does that sound about right?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Arkadiy Maksimovskiy" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Samstag, 2. Juli 2016 18:36:51
> Betreff: Re: [Freesurfer] controlling for total gray matter volume
>
> Hi Clara,
>
> If I am understanding your question correctly, you don't need to control
>for brain volume when looking at thickness analyses.
>
> See quote below from this link:
>
> http://www.freesurfer.net/fswiki/eTIV
>
> "Note that this correction is only useful in situations where the
>structure scales with head size. Outside of this, correction just adds
>noise, or provides inaccurate data. In the case of the measures from
>Freesurfer, one would apply correction to the volume measures and not
>thickness measures. This is because volume scales with head size which is
>mostly due to changes in surface area, whereas thickness alone scales to
>a much less degree."
>
> Best,
> Arkadiy
>
> On Sat, Jul 2, 2016 at 12:00 PM, <
>freesurfer-requ...@nmr.mgh.harvard.edu > wrote:
>
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. controlling for total gray matter volume (Clara K?hn)
> 2. cotrolling for total gray matter volume (Clara K?hn)
>
>
> --
>
> Message: 1
> Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] controlling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 600644700.119350.1467292783757.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control
>for total gray matter volume. Should I use that information from the
>CROSS before anything has been registered and smoothed or from the LONG
>after they have been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter
>volume when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
> --
>
> Message: 2
> Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] cotrolling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 1473114832.117985.1467291666701.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control
>for total gray matter volume. Should I use that information from the
>CROSS before anything has been registered and smoothed or from the LONG
>after they have been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter
>volume when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
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Re: [Freesurfer] longitudinal tracula

[Harms, Michael]

So, what bvec/bvec file should be associated with the BASE scan?  It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.

I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study, the same issue applies, even if you use all frames “as is”.  In
that case, the potential bias would be due to using data of differing
quality across sessions.  In a sense, we are just making the issue
explicit by discarding bad frames as part of a QC step.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.

However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent as possible
across time points. If you find that there's a longitudinal change, would
this be because there were different directions/b-values in each time
point or because of an actual change in the brain? I suppose that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.

Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:

>
> Hi Anastasia,
> Looking through the trac-preproc and trac-paths scripts, it is now clear
>to me that all the time points for a given subject have to be
>contained/specified
> within the same dmrirc configuration file in order to implement a
>longitudinal TRACULA analysis.  So, I've answered my previous question in
>that regard.
>
> The challenge in our case is that we have separately pre-processed the
>dMRI data for each subject and time point, removing bad frames/volumes
>(using the
> DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the
>time points of a given subject.  We can specify the bvec file for each
>subject/time
> point using the bveclist configuration parameter.  But there is no
>analog available for bvals, since only a single bvalfile can be
>specified.
>
> I see that this issue has been raised in a couple other posts relatively
>recently (2015):
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
> but no working solution was provided at that time.
>
> I’m wondering if there is perhaps now a development version of TRACULA
>that supports a “bvallist” capability?  If not, it doesn’t look like it
>would be too
> difficult to modify trac-all  to include that capability (modeling after
>what is already in trac-all for the bveclist/bvecfile stuff).  But, in
>that case,
> it isn’t immediately clear to me if there are other downstream “gotchas”
>in the preproc, paths, or stats stage specific scripts/binaries that
>would need
> modifications as well.  [I don’t see anything in the sections related to
>the BASE-specific processing in trac-preproc involving bvals/bvecs, so
>think we are
> fine there.  But it is harder for me to tell what is going on in
>trac-paths].
>
> thanks,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From:  on behalf of "Harms,
>Michael" 
> Reply-To: Freesurfer support list 
> Date: Wednesday, June 29, 2016 at 5:00 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] longitudinal tracula
>
>
> Hi,
> When running TRACULA with longitudinal data, is it necessary for all
>scan waves of a given subject to be included in a single dmrirc file?  My
>initial
> thought was “no”, that it would be fine to run one scan wave per subject
>per dmrirc file (as long as the “baselist” variable is set appropriately
>for each
> scan wave and subject).
>
> But looking at the ‘trac-all’ script, I see
>
> if ($#baselist == 0) then#--->>> A single time point for each subject
> …
> else#--->>> Multiple time points for each subject
> …
>
> So, I’m wondering why different sections in the code would be necessary
>if in fact it i

Re: [Freesurfer] longitudinal tracula

[Harms, Michael]

Hi Anastasia,
Looking through the
trac-preproc and
trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified
 within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis.  So, I've answered my previous question in that regard.




The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool).
  Thus, the bvecs/bvals are not identical for all the time points of a given subject.  We can specify the bvec file for each subject/time point using the
bveclist configuration parameter.  But there is no analog available for bvals, since only a single
bvalfile can be specified.  




I see that this issue has been raised in a couple other posts relatively recently (2015):

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html

but no working solution was provided at that time.



I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist”
 capability?  If not, it doesn’t look like it would be too difficult to modify 
trac-all  to include that capability (modeling after what is already
 in trac-all for the
bveclist/bvecfile
stuff).  But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries
 that would need modifications as well.  [I don’t see anything in the sections related to the BASE-specific processing in
trac-preproc involving bvals/bvecs, so think we are fine there.  But it is harder for me to tell what is going on in
trac-paths].




thanks,

-MH





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu








From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula







Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.





 



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[Freesurfer] longitudinal tracula

[Harms, Michael]

Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then
#--->>> A single time point for each subject
…
else
#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
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Re: [Freesurfer] Quality control with different pipelines

[Harms, Michael]

Yes on all fronts.




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie Whitaker <kw...@cam.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 22, 2016 at 8:55 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Quality control with different pipelines







Thank you Michael!

So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent
 on checking again as you recommend) have a well edited subject who can now be reported as having been processed with the dev version, right?


Thanks again

Kx


On 22 June 2016 at 14:48, Harms, Michael 
<mha...@wustl.edu> wrote:





Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
 under the new FS version.


And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie Whitaker <kw...@cam.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 22, 2016 at 1:28 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Quality control with different pipelines












Hi everyone,


I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also
 applies to moving to v 6 when it is released).


If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted?
 Or does this "shortcut" not do what I think it does?


Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?


Thank you again for the fantastic tools!


Kx






-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com
















 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44

Re: [Freesurfer] Quality control with different pipelines

[Harms, Michael]

Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
 under the new FS version.


And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Kirstie Whitaker 
Reply-To: Freesurfer support list 
Date: Wednesday, June 22, 2016 at 1:28 AM
To: Freesurfer support list 
Subject: [Freesurfer] Quality control with different pipelines










Hi everyone,


I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also
 applies to moving to v 6 when it is released).


If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted?
 Or does this "shortcut" not do what I think it does?


Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?


Thank you again for the fantastic tools!


Kx






-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com














 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] 2 unrelated questions regarding structural data

[Harms, Michael]

Hi Josh,
The WU-UMN HCP outputs provide the thickness values already aligned to a common mesh in the *thickness.{32,164}k_fs_LR.dscalar.nii files (both 32k and 164k mesh version available).  You  should be able to run a nice, permutation-based group analysis on
 those using the FSL PALM tool.  If you run into problems in that regard, please let us know your experience on the HCP-Users list.


Alternatively, if you want to use FS-specific tools to run the group analysis, the entire FS output, in the standard FS format, is available as part of the “Structural Extended” packages.  If you download those, the only small additional step you would
 need to do would be to create a “SUBJECTS_DIR” like directory which contains sym-links pointing to the location of the FS data in the HCP file structure.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Josh Gray 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Friday, May 13, 2016 at 8:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] 2 unrelated questions regarding structural data









Hello,


1) I am working with the recent release of human connectome data and am trying to run group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want
 to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for the pipeline to run properly. Since I did not run recon-all locally, their file arrangement is unique, many files are zipped, etc. Therefore the
 scripts (e.g., mris_preproc) do not know where to look, as they do with the typical file structure. Can you tell me what specific files this pipeline needs to generate the GLM? Alternatively, if you have performed this process with the human connectome data
 you can tell me which directories/files need to be unzipped and placed in SUBJECTS_DIR. Just need to know what specific files the scripts in the group analysis pipeline are searching for when I run them.


2) I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right
 hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website).
 Is there a quick way to do this?


Thank you for your help!

Josh





-- 




Graduate Student 
Psychology Dept. - Clinical Program
Experimental & Clinical Psychopharmacology Laboratory
University of Georgia
















 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] does lGI needs correction for any global measure?

[Harms, Michael]

Hi,
There are certainly papers in which thickness is corrected using global mean thickness, and surface area is corrected using total surface area.  It is a valid approach, and one that I think is preferable to correcting by using a somewhat arbitrary adjustment
 to a non-like measure.


Re (3):  If you wish, you can compute your “global” covariate for surface area or thickness excluding the contribution of the region that you are testing.  Then, the covariate is for the “rest of the brain”, and not impacted by the contribution from the
 region that you are testing.


We have done both these things in the following:
http://www.ncbi.nlm.nih.gov/pubmed/20118463


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of maaike rive 
Reply-To: Freesurfer 
Date: Friday, May 6, 2016 at 3:53 AM
To: Freesurfer 
Cc: "marie.sch...@unige.ch" 
Subject: Re: [Freesurfer] does lGI needs correction for any global measure?






Hi Doug,
 
Thanks for the reply.
I'm still struggling with this issue though. 
 
1. For instance, if one corrects surface area for ICV in the GLM, shouldn't the fact that this relationship is non-linear be taken into account? Since volume increases with r^3 and surface with r^2... Same goes for lGI, how is the relationship
 between lGI en ICV?
 
2. If I choose to correct for TSA, it seems natural to correct thickness for mean (or total) thickness and lGI for some global measure (is there such thing as mean or total lGI?) as well, or am I mistaken? I don't understand why one measure should
 be corrected for a global measure with the same units, whereas another should not.
 
3.  ICV is not influenced by the volumes of the different brain structures (it is not a summation of these volumes) so volume correction for ICV is unbiased. However TSA (or mean thickness, or "global lGI measure") is dependent of the area (or
 thickness or lGI) of each discrete brain structure, right? So for instance if one group has a smaller superior frontal area, total area will be smaller as well. Wouldn't correction remove part of the effect then?

 
Maaike
 
 
 

 
> To: freesurfer@nmr.mgh.harvard.edu;
marie.sch...@unige.ch
> From: gr...@nmr.mgh.harvard.edu
> Date: Thu, 5 May 2016 12:32:11 -0400
> Subject: Re: [Freesurfer] does lGI needs correction for any global measure?
> 
> 
> 
> On 05/02/2016 07:39 AM, maaike rive wrote:
> > Dear freesurfer experts,
> > 
> >
> >
> > 
> > I have a question regarding correction of cortical measures or global 
> > measures (ICV, total surface area). As I understand from literature 
> > and the freesurfer wiki, a model for thickness should not be corrected 
> > for ICV (since thickness does not scale with total brain volume), but 
> > surface area should be corrected since is does scale with total brain 
> > volume. Three questions:
> >
> > 
> >
> >
> > 
> > 1. should I use ICV or should I use total surface area (TSA) as 
> > covariate in the model to correct surface area (by the way, average 
> > ICV and TSA do not differ between the groups to compare )?
> >
> > 
> Not sure. They will be different models. ICV should not change over the 
> lifetime whereas total surface area will.
> > 
> > 2. does lGI also need correction? does it scale with volume? If so, do 
> > I need to correct for ICV or for TSA? Usually I see no correction but 
> > some do use ICV...
> >
> > 
> I don't know, perhaps Marie will weigh in
> > 
> > 3. even if the average of certain measures (like ICV/TSA, or gender, 
> > or age) does not differ between groups, should they be added to the 
> > model? If I do not correct for gender, for example, my results change 
> > and most papers do use age and gender as covariates if they compare 
> > groups despite a lack of differences between groups...
> >
> > 
> They can still reduce intersubject variance.
> doug
> > 
> >
> >
> > 
> > Thanks,
> >
> > 
> >
> >
> > 
> > Maaike
> >
> > 
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
ftp://surfer.nmr.mgh.h

Re: [Freesurfer] white matter edits not incorporated

[Harms, Michael]

That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).

I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.

Has this been fixed in the forthcoming FS 6.0?

thanks,
-MH

 snip 

ok, I see what's going on. Here is the sequence of calls:

1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh

Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.

2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh

internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.

The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.

I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses
the
white surface that the user can see and things should be consistent

Bruce

 end-snip 



--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgw"  wrote:

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can
give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
> Hi Bruce,
>
> Thanks! I'll give it a whirl.
>
> d
>
> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>  wrote:
>> Hi Daniel
>>
>> the problems isn't that it it's ignoring the wm edits, it is that it
>>starts
>> the orig surface out there, but then retracts to the (same) visible
>> gray/white boundary that it found in the first place. For this type of
>> lesion I think what you should do is also edit those voxels in the
>>aseg.mgz
>> and change them to right-lesion. This should freeze the white surface
>>there
>> I think. If it doesn't, let me know and I'll fix it.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Here is the log for the most recent -autorecon2-wm call:
>>>
>>> Thanks!
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>>  wrote:
 can you send us the recon-all.log? I don't see an obvious reason why
it
 wouldn't have worked
 On Tue, 19 Apr 2016, dgw wrote:

> Just to follow up, I have tried several different options with
> recon-all to get the white matter edits to stick on this participant,
> and it doesn't seem to be working:
>
> re-editing wm.mgz and running recon-all -autorecon2-wm
> re-editing wm.mgz and running recon-all -make all
>
> I can't seem to get any appreciable change in the white matter
> surface. I have attached a screenshot, for an example.
>
> hth
> d
>
>
> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>> Hi,
>>
>> I recently edited a brain with a gyral cyst, carefully filling the
>> cyst with white matter in the wm.mgz. Unfortunately after running:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>
>> none of the edits were incorporated.
>>
>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>
>> Is there some other misake?
>>
>> I followed this guide
>>
>>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
>>_freeview
>>
>> Thanks,
>> Dan
>
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 The information in this e-mail is intended only for the person to
whom it is
 addressed. If you believe this e-mail was sent to you in error and
the e-mail
 contains patient information, please contact the Partners Compliance
HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
you in error
 but does not contain patient information, please contact the sender
and properly
 dispose of the e-mail.

>>>
>> ___

Re: [Freesurfer] Oblique Slice Acquisition

[Harms, Michael]

Just an aside: if you acquire oblique (e.g. AC/PC aligned), and don’t want
FS to rotate the volume back into the native scanner space as part of its
“conformation” step, you can edit the s/qform of the NIFTI header to
appear as a non-oblique acquisition.  As Bruce noted, this isn’t a big
deal, although avoiding the rotation in the conformation step does
eliminate a resampling during the conformation step which will blur/smooth
the data to a small degree.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/13/16, 12:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Kate

I don't think that will matter. Try running it through from the original
dicoms and see if things seem accurate. That isn't actually an artifact,
it just looks strange because of the slight angle of the view. My guess is
we will handle this fine

cheers
Bruce

On Wed, 13 Apr
2016, Katherine Reiter wrote:

> Hello freesurfer experts,
> I am working with a dataset that was acquired with oblique slices
>aligned to
> each participant's ac-pc line.
>
> 1) I've run a handful of subjects through mri_convert and the recon
>stream
> and each subject has a slight abnormality in the ventral temporal
>regions.
> It's subtle but apparent in each acquisition (image attached and the
> abnormality is apparent at the red cross). We believed it to be an
>alignment
> issue due to the oblique slices. Is there any way to fix this
>abnormality?
>
> 2) Are there any different preprocessing steps that should be added to
> mri_convert or the recon stream?
>
> Thanks much in advance!
> Kate
>
>
> Katherine Reiter, M.S.
>
> Clinical Psychology Doctoral Student
>
> Marquette University
>
> Phone: (414) 288-3807Email: katherine.rei...@marquette.edu
>
>
>



The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] Ris: eTIV question

[Harms, Michael]

That is, going back to your earlier post, I personally don’t find it all
that interesting whether a given brain area is atrophic relative to head
size, especially in the situation where many regions are atrophic (i.e.,
global atrophy).  I’m more interested in knowing whether the atrophy in a
given region is greater (or less than) what would be predicted based on
the global atrophy.

cheers,
-MH
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 10:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Harms, Michael"  wrote:

Even assuming one had a true measure of TIV, if you get meaningfully
different results when using TIV vs. brain size as a covariate, isn’t that
a rather important thing to point out?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Angela

yes, although if the eTIV is (incorrectly) correlated with atrophy you
may be removing some of your effect (and slightly reducing your power)

cheers
Bruce
On
Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:

> Hi Bruce,
> this is true, but I noticed that many papers used TIV as a covariate. In
> addition, in my samples (both pathological and healthy) there is a
> moderate positive correlation between gyrification and TIV (and brain
> volume). For the hemispheric overall gyrification index the correlation
>is
> 0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
> I think that in pathological samples with possible brain atrophy, this is
> a way to control for a possible bias effect. Am I wrong?
>
> Thank you
> Angela
>
>> Hi Angela
>>
>> gyrification is the ratio of areas and hence dimensionless, so I would
>> think it wouldn't be much affected by TIV.
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>>
>>> In the case of a gyrification analysis, does correction for total brain
>>> volume make sense?
>>>
>>> Angela
>>>
>>> Inviato dal mio dispositivo Huawei
>>>
>>>  Messaggio originale 
>>> Oggetto: Re: [Freesurfer] eTIV question
>>> Da: Bruce Fischl
>>> A: Freesurfer support list
>>> CC:
>>>
>>>
>>>   yes, it's a somewhat different and more conservative test. I
>>>   guess you
>>>   could check the talairach transforms of some of your subjects
>>>   with eTIVs
>>>   that don't make sense (or change the most over time) to try to
>>>   see why
>>>   this is happening. Or take Mike's suggestion and test a
>>>   different (but
>>>   probably still interesting) hypothesis
>>>
>>>   On Sun, 21 Feb 2016, Angela Favaro wrote:
>>>
>>>  > Hi, thank you
>>>  > I think this would test something different: 'how much a brain
>>>   area is
>>>  > atrophic controlling for the average brain atrophy' and not
>>>   'how much
>>>  > a brain area is atrophic controlling for the individual
>>>   differences in
>>>  > head size'. Doesn't it?
>>>  >
>>>  > Angela
>>>  >
>>>  >
>>>  > "Harms, Michael" ha scritto:
>>>  >
>>>  >> Hi,
>>>  >> Why not use a measurement of brain size rather than “eTIV”?
>>>  >>
>>>  >> cheers,
>>>  >> -MH
>>>  >>
>>>  >> --
>>>  >> Michael Harms, Ph.D.
>>>  >>
>>>  >> ---
>>>  >> Conte Center for the Neuroscience of Mental Disorders
>>>  >> Washington University School of Medicine
>>>  >> Department of Psychiatry, Box 8134
>>>  >> 660 South Euclid Ave.Tel: 314-747-6173
>>>  >> St. Louis, MO 63110Email: mha...@wustl.edu
>>>  >>
>>>  >>
>&

Re: [Freesurfer] Ris: eTIV question

[Harms, Michael]

Even assuming one had a true measure of TIV, if you get meaningfully
different results when using TIV vs. brain size as a covariate, isn’t that
a rather important thing to point out?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Angela

yes, although if the eTIV is (incorrectly) correlated with atrophy you
may be removing some of your effect (and slightly reducing your power)

cheers
Bruce
On
Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:

> Hi Bruce,
> this is true, but I noticed that many papers used TIV as a covariate. In
> addition, in my samples (both pathological and healthy) there is a
> moderate positive correlation between gyrification and TIV (and brain
> volume). For the hemispheric overall gyrification index the correlation
>is
> 0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
> I think that in pathological samples with possible brain atrophy, this is
> a way to control for a possible bias effect. Am I wrong?
>
> Thank you
> Angela
>
>> Hi Angela
>>
>> gyrification is the ratio of areas and hence dimensionless, so I would
>> think it wouldn't be much affected by TIV.
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>>
>>> In the case of a gyrification analysis, does correction for total brain
>>> volume make sense?
>>>
>>> Angela
>>>
>>> Inviato dal mio dispositivo Huawei
>>>
>>>  Messaggio originale 
>>> Oggetto: Re: [Freesurfer] eTIV question
>>> Da: Bruce Fischl
>>> A: Freesurfer support list
>>> CC:
>>>
>>>
>>>   yes, it's a somewhat different and more conservative test. I
>>>   guess you
>>>   could check the talairach transforms of some of your subjects
>>>   with eTIVs
>>>   that don't make sense (or change the most over time) to try to
>>>   see why
>>>   this is happening. Or take Mike's suggestion and test a
>>>   different (but
>>>   probably still interesting) hypothesis
>>>
>>>   On Sun, 21 Feb 2016, Angela Favaro wrote:
>>>
>>>  > Hi, thank you
>>>  > I think this would test something different: 'how much a brain
>>>   area is
>>>  > atrophic controlling for the average brain atrophy' and not
>>>   'how much
>>>  > a brain area is atrophic controlling for the individual
>>>   differences in
>>>  > head size'. Doesn't it?
>>>  >
>>>  > Angela
>>>  >
>>>  >
>>>  > "Harms, Michael" ha scritto:
>>>  >
>>>  >> Hi,
>>>  >> Why not use a measurement of brain size rather than “eTIV”?
>>>  >>
>>>  >> cheers,
>>>  >> -MH
>>>  >>
>>>  >> --
>>>  >> Michael Harms, Ph.D.
>>>  >>
>>>  >> ---
>>>  >> Conte Center for the Neuroscience of Mental Disorders
>>>  >> Washington University School of Medicine
>>>  >> Department of Psychiatry, Box 8134
>>>  >> 660 South Euclid Ave.Tel: 314-747-6173
>>>  >> St. Louis, MO 63110Email: mha...@wustl.edu
>>>  >>
>>>  >>
>>>  >>
>>>  >>
>>>  >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
>>>   on behalf of
>>>  >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
>>>  >>
>>>  >> there is a mistake in the graph, hippocampal volume is TIV2
>>>  >> I apologize for that!
>>>  >>
>>>  >> Angela Favaro ha scritto:
>>>  >>
>>>  >>> Hi Bruce,
>>>  >>> please find attached the graph of the correlation between
>>>   the two time
>>>  >>> point. I did not find outliers or failures. However the
>>>   disc

Re: [Freesurfer] eTIV question

[Harms, Michael]

Hi,
Why not use a measurement of brain size rather than “eTIV”?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Angela Favaro"  wrote:

there is a mistake in the graph, hippocampal volume is TIV2
I apologize for that!

Angela Favaro  ha scritto:

> Hi Bruce,
> please find attached the graph of the correlation between the two time
> point. I did not find outliers or failures. However the discrepancy
> between TIVs is particularly high in few cases. Obviously these data
> are those before running longitudinal streaming
> This is a sample of adolescents with low body weight (anorexia nervosa).
> In my previous study (on young adults with low weight) I found no
> correlation between TIV and body weight and high correlations between
> fs estimated TIV and manually segmented TIV (r=0.94 in the whole
> sample and r=0.93 in the underweight sample (n=38)).
> Do you think that the young age can be a factor? or patients who are
> more acutely underweight?
> Thank you for any suggestion
>
> Angela
>
>
> Bruce Fischl  ha scritto:
>
>> Hi Angel
>>
>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure
>> that there aren't outliers/failures in that set?
>>
>> Bruce
>>
>>
>> On Sun, 14 Feb 2016, angela.fav...@unipd.it wrote:
>>
>>> Dear Freesurfer experts,
>>> I have a question about eTIV (FS 5.3) which I use as a covariate where
>>> appropriate. Is it in some way influenced by the presence of brain
>>> atrophy?
>>> I have a new sample of subjects in a longitudinal study: at time 1 they
>>> have some atrophy (due to low body weight) that improves in time 2 (4
>>> months). I observed that eTIV-time1 is slightly correlated with weight
>>> (r=0.3) whereas no correlation is present at time 2. The correlation
>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected
>>>(r=0.53)
>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2
>>> (0.65).
>>>
>>> Do you suggest in these cases to perform manual segmentation to obtain
>>> TIV? or is there any other method (in freesurfer) to obtain an
>>>estimate of
>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV?
>>>
>>> Thank you for any suggestion
>>>
>>> Angela
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
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Re: [Freesurfer] DTI - Tracula question

[Harms, Michael]

As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects.  If the orientation was customized
 individually for each subject (e.g., to align the imaging plane with the AC/PC), then it is unlikely that using a single table for all subjects is appropriate.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Alan Francis 
Reply-To: Freesurfer support list 
Date: Friday, February 5, 2016 at 3:57 PM
To: Anastasia Yendiki 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] DTI - Tracula question








Hi Anastasia:


Thank you so much. Yes that is very helpful.


best,


Alan


On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki 
 wrote:


Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they
 are. If there are only very small differences, using a single table for all will not make a difference.

Hope this helps,

a.y



On Fri, 5 Feb 2016, Alan Francis wrote:


Thanks Anastasia - that was very helpful. I have another question :  I am working on a DTI dataset of around 70 subjects. This
dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been
acquired on the same scanner?

 

thanks,

 

Alan


On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki  wrote:

      Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti
      volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and
      b-value table as separate files.

      Run "mri_convert --help" to see all image file formats that we can handle.

      Hope this helps,
      a.y

      On Wed, 3 Feb 2016, Alan Francis wrote:

            Hi Anastasia:

            I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single
            nii.gz file. The BVECS and
            BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?

            Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?

            thank you so much,

            best regards,

            Alan

            --
            |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

            Alan N. Francis PhD
            NIDA T32  Fellow in Computational Neuroscience
            Brain Imaging Center
            McLean Hospital
            Harvard Medical School
            115 Mill Street, Belmont, MA 02478
            al...@bwh.harvard.edu
            afran...@mclean.harvard.edu
                                                                                                                      
            |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|









-- 




|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscie

Re: [Freesurfer] Question about Intracranial Volume

[Harms, Michael]

Hi Pietro,
One additional thing to consider is that the ICV (eTIV) is entirely
dependent on the Talairach transform.  Frequently, the accuracy of
Talairach transform isn¹t explicitly checked by users, because the
surfaces, aseg, etc can be accurate even if the Talairach transform isn¹t.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/11/16, 7:43 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Pietro

ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
his paper. Correcting for whole brain volume is certainly a reasonable
thing to do but note that then you are testing a somewhat different
hypothesis (that local atrophy is faster than whole-brain atrophy, as
opposed to whether atrophy exists at all)

cheers
Bruce


On Mon, 11 Jan 2016, pietro de rossi wrote:

> Dear FreeSurfers,
> I am editing a paper on subcortical volumes in deficit schizophrenia
>after
> some reviewers' comments.
> On of them suggested me to correct the volumes of subcortical structures
>for
> whole brain volume instead of intracranial volume. In the reviewer's
>opinion
> ICV  estimated by FreeSurfer 5.1 has a bad quality and is not reliable.
> However,  neither the reviewer provides any evidence, nor I could find
> any...
> Is there any evidence for this?
>
> Thanks in advance,
>
> Pietro
>
> --
> Pietro De Rossi, MD
> -
> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
>Dipartimento
> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>
> NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
> School of Medicine and Psychology, Sapienza University, Sant¹Andrea
> Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
>
> Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
> Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
> Roma
>
> Tel. +39 (0)6 51501358
>
> Fax +39 (0)6 90280774
>
> web: http://www.neuropsichiatrialab.com
>



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Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

[Harms, Michael]

It seems problematic to me to use a nightly dev build for publication.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Matthieu Vanhoutte 
Reply-To: Freesurfer support list 
Date: Tuesday, December 15, 2015 11:13 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta









Hi Bruce,


Is it better to overestimate than underestimate ? Please find joined this two saggital images (FS v5.3 and FS v6_beta) of brain segmentation. Cerebellum in v6_beta really seems to go outside of its borderlines even if cerebellum in v5.3 is indeed lightly underestimated.


Looking at the cerebral cortex I found the segmentation less "smoothed" in v6_beta (with more irregularities near pial surface) than in v5.3 according to coronal views of segmentations joined.



What do you think about it ?  Would you advise me to go on with the v6_beta anyway ?


Would it be better and coherent to use a more recent "nightly dev builds" of FreeSurfer for future publication ?


Thanks in advance for helping !



Best regards,


Matthieu

2015-12-15 17:38 GMT+01:00 Bruce Fischl 
:

Hi Matthieu

I think 6.0 looks better overall, even in the beta that you have. The 5.3
segmentation looks like it is underestimating cerebellum and hippocampus to
me.

cheers
Bruce



On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:

> Dear FS's experts,
>
> I have tried the recon-all process on one subject with both FS v5.3 and v6_beta.
>
> Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other
> structures as cerebellum, hippocampus, ...
>
> I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions.
>
> Could you please look at it and tell me what do you think about and advise me ?
>
> Thank you !
>
> Best regards,
> Matthieu
>
>


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Re: [Freesurfer] QA tools

[Harms, Michael]

In my experience, none of the quantitative "SNR/CNR" metrics available
through various FS tools (some of which may be part of the QATools)
replace the need to manually  inspect the results.  Some truly awful data
may show up as "outliers", but you can't count on those values to flag all
the data with problems.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 11/23/15 11:16 AM, "angela.fav...@unipd.it" 
wrote:

Hi all,

I am starting to use QAtools in Freesurfer.
The scripts are working well, but I have two problems:

1. the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference
or link about how to interpret these data? Or do I only need to look at
outliers (or something similar)? My values are in the range between 19 and
25 (and the subject with 19 have problems at visual inspection).
The script also outputs 'no outlier' in all my subjects. Which type of
outliers is it referring to?

2. I have also problems in getting snapshots, but I think this is due to my
poor experience with setting paths of ImageMagick. I am using a MAC OSX
10.6.8 and I used (tcsh)
setenv MAGICK_HOME /Applications/ImageMagick-6.9.2/bin
but probably this is not enough (any suggestion is greatly apreciated).

Thank you for any help you can give me

Best wishes

Angela




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contains patient information, please contact the Partners Compliance
HelpLine at
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The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

My experience, which appears to be consistent with Doug's, is that there is no substitute for reviewing the images and FS results manually.  Ultimately, it is a bit of a judgement call, and interacts with the goals/purposes of your study.




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: John Anderson <j.ander...@publicist.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 19, 2015 11:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR






Thanks MH,
Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.
Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help
 a lot!
 
any suggestions?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
 
 

Sent: Monday, October 19, 2015 at 12:24 PM
From: "Harms, Michael" <mha...@wustl.edu>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR



 
At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't
 be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.
 
cheers,
-MH
 


-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu


 

From: John Anderson <j.ander...@publicist.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR
 



Hi All,
Thank you very much for your comments!
 
Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
  
  

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR
This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual r

Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't
 be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: John Anderson <j.ander...@publicist.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR






Hi All,
Thank you very much for your comments!
 
Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
 
 

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR
This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/

Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

Hi,

FWIW, I've looked at a number of these measures in 500+ subjects from HCP
data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
relate to each other, and whether they correlate with mean cortical
thickness, white matter surface area, or number of SurfaceHoles (prior to
topology correction).

I didn't find much of note.  e.g., the highest correlations were:

r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
r = -0.25 between white surface area and wmanatsnr
r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
norm.mgz)

Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
0.49).

G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97

In another context (but smaller number of subjects), I've looked to see if
these various snr, cnr measures from FS were related to manual quality
ratings, and the relationship was rather weak.

All-in-all, I haven't seen much that would indicate that these measures
can be used as a sort of "automated" QC measure.  Manual review of the
structurals and FS results is still needed.

That said, the structurals from the HCP 500 release were all of reasonably
good quality to begin with.  So, it is possible that these snr/cnr
measures might be more informative in identifying truly awful scans in a
clinical population with a wider variability in MPRAGE scan quality.

I'd certainly be interested in hearing from anyone if they have found that
to be the case in their data.

BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
orig.mgz and norm.mgz respectively.
Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:

probably similar, although maybe Doug can comment. You probably want to
run
it on the orig.mgz as the intensity normalization can artificially
increase
the SNR (which is kind of the point)
Bruce


On Mon, 19 Oct 2015, John
Anderson wrote:

> Hi Bruce,
> Thanks a lot!! this is really great!
> I ran the command as the following :
>
> mri_cnr subj_01/surf subj_01/mri/norm.mgz
> processing MRI volume subj_01/mri/norm.mgz...
> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
> gray/white CNR = 2.291, gray/csf CNR = 0.848
> lh CNR = 1.569
> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
> gray/white CNR = 2.278, gray/csf CNR = 0.798
> rh CNR = 1.538
> total CNR = 1.554
>
>
> I noticed that the normal range for the SNR  (15-20) when using the
>command
> "wm-anat-snr"
>
> What is the normal range for cnr generated by the binary "mri_cnr"?
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
> Sent: Monday, October 19, 2015 at 8:36 AM
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Cc: j.haen...@psychologie.uzh.ch
> Subject: Re: [Freesurfer] MPRAGE SNR
> Hi John
>
> there is also a binary called mri_cnr that will compute the
> contrast-to-noise ratio (CNR), which is really the more interesting
> metric. It will also spit out the WM means+- std, and the ratio of these
> two can be used as an SNR measure.
>
> cheers
> Bruce
>
>
> On Mon, 19 Oct 2015, John Anderson wrote:
>
> > Dear Jürgen
> > This really helps!
> > I highly appreciate your input on this.
> >
> > Bests,
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> > Sent: Monday, October 19, 2015 at 1:30 AM
> > From: JuergenHaenggi 
> > To: "Freesurfer support list" 
> > Subject: Re: [Freesurfer] MPRAGE SNR
> > Dear John
> > FS's QA tools provide the SNR
> > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
> >
> > there is also a FS function called wm-anat-snr that can be used for
>that.
> >
> > Hope this helps
> > Cheers
> > Jürgen
> >
>
>>-
>>--
>
> > --
> > Jürgen Hänggi, Ph.D.
> > Division of Neuropsychology
> > Institute of Psychology
> > University of Zurich
> > Binzmuehlestrasse 14, PO Box 25
> > 8050 Zurich, Switzerland
> > 0041 44 635 73 97 (phone office)
> > 0041 76 445 86 84 (phone mobile)
> > 0041 44 635 74 09 (fax office)
> > BIN 4.D.04 (office room number)
> > j.haen...@psychologie.uzh.ch (email)
> > http://www.psychologie.uzh.ch/neuropsy/ (website)
> > http://www.juergenhaenggi.ch (private webs

Re: [Freesurfer] Custom parcellation for HCP data

[Harms, Michael]

Hi Simon, 
Since you are using the HCP data, this may be more appropriate for the HCP-Users list.


If you look at the current HCP pipeline code, you'll see that after converting FS surfaces to .surf.gii (using 'mris_convert'), an affine transform is then
applied based on the c_ras contents (applied using 'wb_command -surface-apply-affine').  i.e., to date, mris_convert has not been applying the volume geometry information.  I believe that an option is going to exist in 'mris_convert'
 in the forthcoming FS release that will save out c_ras corrected surfaces.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Simon Baker 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, October 5, 2015 1:12 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Custom parcellation for HCP data






Hi all,


We want to create a custom parcellation for use with the connectome project data. However, we have not been able to achieve accurate spatial alignment between the random parcellation volume and the T1w volume. Specifically, there appears to be an "offset,"
 possibly due to a mismatch between the origin of these volumes. In the following we describe the relevant steps of our pipeline. Please suggest any changes that might help to resolve the issue.


1. Create a high-resolution annotation (parcellation) by randomly parcellating the fsaverage surface into N regions of approximately equal volume.


2. Map the annotation from the source subject (fsaverage) to the target subject using mri_surf2surf.


mri_surf2surf --srcsubject fsaverage --hemi lh --sval-annot highres.annot --trgsubject ${SUBJECTID} --srcsurfreg sphere.reg --trgsurfreg ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.sphere.native.surf.gii --tval lh.highres.annot


[repeat for rh]


3. Obtain vertices and faces data from ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.white.native.surf.gii


[repeat for rh]


4. Using the vertices and faces data obtained in step 3 as inputs for the write_surf Matlab function, create the lh.white surface file.


[repeat for rh]


5. Obtain thickness data from ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.thickness.native.shape.gii


[repeat for rh]


6. Convert the annotation into a volume using mri_label2vol.


mri_label2vol --annot lh.highres.annot --temp ${SUBJECTS_DIR}/${SUBJECTID}/T1w/T1w_acpc_dc_restore.nii.gz --identity --proj frac 0 1 .1 --subject ${SUBJECTID} --hemi lh --o vol_lh.nii


[repeat for rh]


7. Configure the volume (remove unwanted ROIs).


[repeat for rh]


8. Combine the configured volumes from each hemisphere to create the random parcellation volume.


9. Overlay the random parcellation volume on the template volume.


See attached screenshot.jpeg showing the misalignment between the random parcellation volume and the template volume.


Kind regards,


Simon Baker

Brain & Mental Health Laboratory
Institute of Cognitive & Clinical Neuroscience

Monash University








 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] total grey matter volume

[Harms, Michael]

They are conveniently already provided for you in the {lh,rh}.aparc.stats files.  And even more conveniently, if you run 'aparcstats2table', with --measure=thickness, the last column is the mean cortical thickness (for that hemisphere), and if you run
 with --measure=area, the last column is the total white surface area (for that hemisphere).


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: , Lena <lena@kcl.ac.uk>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, September 29, 2015 6:52 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] total grey matter volume








Thanks, Michael. How do I get the total thickness and total surface area values form Freesurfer/Qdec please?
 
Thanks again,
L
 


From:
freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
On Behalf Of Harms, Michael
Sent: 29 September 2015 04:30
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] total grey matter volume


 



 


I'm a fan of using global mean thickness as a covariate for thickness analyses, and total surface area as a covariate for surface area analyses.  That way you directly covary for possible global
 effects using the same type of measure that you are analyzing.


 


cheers,


-MH


 




-- 


Michael Harms, Ph.D.



---


Conte Center for the Neuroscience of Mental Disorders


Washington University School of Medicine


Department of Psychiatry, Box 8134


660 South Euclid Ave. Tel: 314-747-6173


St. Louis, MO  63110 Email:
mha...@wustl.edu





 


From: Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, September 28, 2015 11:18 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] total grey matter volume


 




Not for  thickness. For surface area it is a good idea to do some kind of normalization. Typically people use the estimated intracranial volume (ICV). You can also use total brain volume or total grey volume. You just need to be aware that each one of these
 tests something different.



On 9/28/15 12:15 PM, Lim, Lena wrote:


 
Dear Experts,
 
Do we need to include total grey matter volume as a covariate in the freesurfer cortical thickness and surface area analyses? I have come across papers that do and don’t; so I am not sure if I have to do that.
 Please kindly advice.
 
Many thanks,
 
Lena
 




___
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.






 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] total grey matter volume

[Harms, Michael]

I'm a fan of using global mean thickness as a covariate for thickness analyses, and total surface area as a covariate for surface area analyses.  That way you directly covary for possible global effects using the same type of measure that you are analyzing.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Doug Greve 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, September 28, 2015 11:18 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] total grey matter volume





Not for  thickness. For surface area it is a good idea to do some kind of normalization. Typically people use the estimated intracranial volume (ICV). You can also use total brain volume or total grey volume. You just need to be aware that each one of these
 tests something different.


On 9/28/15 12:15 PM, Lim, Lena wrote:





 
Dear Experts,
 
Do we need to include total grey matter volume as a covariate in the freesurfer cortical thickness and surface area analyses? I have come across papers that do and don’t; so I am not sure if I have to do that. Please kindly advice.
 
Many thanks,
 
Lena

 


 
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Re: [Freesurfer] running dt_recon on a philips Achieva DTI dataset;

[Harms, Michael]

That depends on a number of complicated, potentially inter-related factors such as:
1) What exactly is Philips putting into that field in its DICOMs
2) Is mri_convert returning a NIFTI with the same orientation as Philips is using for its gradient directions.
3) Importantly, if the acquisitions are acquired in an oblique plane, is the Philips entry in the DICOMs rotated into the image space, or reported in the scanner space.


I find it helpful to:
1) Compare to the output of other converters -- e.g., have you tried using 'dcm2nii'?
2) Run a tensor model with what you think are the correct set of directions, and then confirm that the direction of the first eigenvector is correct throughout the white matter tracts.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Mehul Sampat 
Reply-To: Freesurfer Mailing List 
Date: Thursday, September 10, 2015 2:22 PM
To: Freesurfer Mailing List 
Subject: [Freesurfer] running dt_recon on a philips Achieva DTI dataset;






Hi Folks, 


I am trying to run dt_recon on a  Philips Achieva
DTI dataset. I could not find an example of a bvecs for this dataset so i made one in this way:


I have 850 dicom slices. mri_convert correctly splits it into 17 nifti files (50 slices each). I took 17 dicom slices with the same ImagePositionPatient and then found the DiffusionGradientOrientation for these 17 slices (the values are below). 
I just wanted to check that: 
1. These are the 17 vectors I should use in the bvecs file for dt_recon ?
2. This is the order i should keep these vectors in ? 
3. I thought there would be 17 unique Diffusion GradientOrientation values; but I only find 16 in the slices (0 0 0) is repeated twice. (One of the slices with (0,0,0) has a bvalue of 0 and while the other has a b-value of 2500)


Mehul
   
           0         0         0
   -0.5000   -0.5000   -0.7071
   -0.5000   -0.5000    0.7071
    0.7071   -0.7071    0.
   -0.1104   -0.7070   -0.6985
    0.2893   -0.6996   -0.6534
    0.6275   -0.3305   -0.7050
    0.6574   -0.2734   -0.7022
   -0.6725   -0.5421   -0.5038
    0.7038   -0.4911    0.5133
   -0.6930   -0.2531    0.6751
   -0.7066   -0.7071    0.0277
   -0.2821   -0.7070    0.6485
    0.2886   -0.7016    0.6514
    0.7058   -0.7063    0.0537
    0.7014   -0.2050    0.6827
         0         0         0






 



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Re: [Freesurfer] ventricular CSF volumes

[Harms, Michael]

Hi,
I would sum up the set of labels you have in (2) if you want the best estimate of ventricular volume.


See the following page for additional info on the various measures:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats


In particular, I would expect your measure in (2) would be much more correlated with
BrainSegVol - BrainSegVolNotVent than 
eTIV - BrainSegVolNotVent


Indeed, the only difference according to the above wiki page between (2) and  BrainSegVol - BrainSegVolNotVent should be that the latter includes voxels labelled as "CSF" in the aparc+aseg.mgz


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Mayer Kristina 
Reply-To: 'Freesurfer support list' 
Date: Thursday, September 10, 2015 1:23 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" , Bruce Fischl
 , 'Freesurfer support list' 
Subject: [Freesurfer] ventricular CSF volumes








 
Dear Freesurfers,
I am calculatig with ventricular volumes in aseg.stats.

1. According to the archives Mail calculation of ventricular CSF is is instructed differently:
- Bruce Fischl 2007 to Jenifer: Add ventricular volumes including CSF (segid 24): Left Lateral Ventricle (segid 4) + Left Inferior Lateral Ventricle (segid 5) + Right
 lateral Ventricle (segid 43) + Right Inf Lateral Ventricle (segid 44) + 3rd Ventricle (segid 14) + 4th Ventricle (segid 15) + 5th Ventricle (segid 72) + CSF (segid 24)

- Bruce Fischl 2007 to Nayoung and 2014: Add choroids plexus to sum of ventricular volumes, but
exclude CSF as in T1 weighted images the CSF cannot be distinguished from bone and would represent sulcal CSF (not ventricular), anyway.
 
>> Which volumes (which segid’s?) shall I include for the total ventricular CSF?
 
2. When I add up following volumes for ventricular CSF:
Left Lateral Ventricle (segid 4) + Left Inferior Lateral Ventricle (segid 5) + Right lateral Ventricle (segid 43) + Right Inf Lateral Ventricle (segid 44) + 3rd Ventricle (segid 14) + 4th Ventricle (segid 15) +
 5th Ventricle (segid 72) + Right choroids plexus (63) + left choroids plexus (31)
and then correlate with the following calculated volume:
eTIV – BrainSegVolNotVent
the correlation is highly significant (p<0.000) but with a correlation of only r=0.66 (n=47)
 
>> Why are the volumes not the same? Which volumes are the reason for the discrepancy.
 
thanks for advice!
 
Cheers, Kristina






 



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Re: [Freesurfer] how to fix errors in 3d mesh

[Harms, Michael]

Sounds like you had a clinical scan and got a copy of a sagittal scan series and an axial scan series.  Those would be "2D" acquisitions in which the slice thickness is probably considerably thicker than the in-plane resolution.  That kind of data isn't
 ideal for FS.  Rather, data for FS is usually collected with what is known as a "3D" sequence, and acquired with isotropic resolution in all 3 axes, typically 1 mm resolution or less.


You're free to try using the AX series if you wish, although it will likely still have "issues" as well.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Alexander van Dijk 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday, August 26, 2015 1:27 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] how to fix errors in 3d mesh





Hi all,


I am an interested neuroscience newbie and I am following this excellent online guide on how to create a 3d print of my cortex using an MRI scan and freesurfer: http://nmarinsek.com/3D-printed-brain/


Sofar, i have been successful in generating the left and right hemispheres based on an eSAG T1 MRI scan (3T) of 32 images, but the right hemisphere appears to have a large hole in the 3d mesh and in general seems to be of less fidelity than the
 left hemisphere:


https://images.shapeways.com/3dviewer/aopt?model=3752203&v=1&raw=false&bClass=printability-center-x3dom&clipping=1&rot=0&key=c2a1314d08f29e38bed8952375ee5fd4


I am wondering what could be the cause of the gap, the lower fidelty in general, and how best to fix it?


Also, after the MRI scan I received both the eSAG T1 scan (32 images), and an eAX T1 (36 images). Would there be any reason to use one over the other, and is it possible to combine these in freesurfer for better quality modeling?


Thank you,
Alexander





 



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Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control

[Harms, Michael]

Hi Martin,
I totally agree that we need robust approaches to either correct for motion during the structurals in real time (as you guys have been working on with your vNav sequence), or start at least quantifying motion during structural imaging (e.g,. again by using
 the same vNav sequence, but just using it to estimate the motion).


It seems challenging to me though, and potentially somewhat arbitrary (i.e., variable across investigators), to start making decisions to exclude scans with moderate to mild movement related ringing, which is such a common problem.  At least not without
 a better understanding of how a given degree of ringing translates to your quantitative X mm/min of motion measurement.  Along those lines, do you guys have any illustrations of what X mm/min of motion looks like in the actual structurals for varying values
 of X?  It would be really helpful for contextualizing your paper if a set of images were available showing that mapping.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 5, 2015 6:55 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Head Motion -- was: surface reconstruction and quality control




Hi Michael, 

we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these
 measurements can be severely biased and most users don't even check their images. We found that 1mm/min of motion reduces gray matter volume by 0.7%. This is a lot, given that the best still scans in our healthy young adult test subjects were at 2-3mm/min
 (that was the no-motion scan). QC was able to remove scans with above 6 or 7mm/min. So on average even after QC and removal of scans with motion problems, you end up having lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM volume. I think, (maybe
 someone here knows better), that is the atrophy of a healthy control in 5 years and probably more than the yearly loss in an advanced AD or HD patient.

Depending on the study, it may very well be possible that the disease group moves more than the control group, the older group more than the younger (unless you have kids, who move a lot) and also longitudinally that motion increases over time. This will bias
 your study. 
You are right, that removing single (worst case) images will not cut it. The problem is far worse. We need a way to either
-correct motion online
-at least quantify motion during structural imaging to use as a covariate or for filtering severe cases.

That is why I recommended to use fMRI or diffusion close to the structural to estimate the motion there. That should give you an idea (of course does not replace manual QC for filtering bad cases). We need to avoid running drug studies that basically quantify
 the amount of reduced motion with an expensive MRI scan.

Anyway, I would say, if in doubt remove it. To at least limit the influence of motion bias to the 3-5% range (which is still too large).

Cheers, Martin



On 08/05/2015 05:44 PM, Harms, Michael wrote:






Hi Emma, Martin,
I'd like to offer a different perspective.  Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case.  If we all started
 excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects.  If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality
 structurals!


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Emma Thompson <vonecono...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 5, 2015 4:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface reconstruction and quality control





Thanks Martin, I will exclude this subject from my analyses.


On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter 
<mreu...@nmr.mg

Re: [Freesurfer] surface reconstruction and quality control

[Harms, Michael]

Hi Emma, Martin,
I'd like to offer a different perspective.  Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case.  If we all started
 excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects.  If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality
 structurals!


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Emma Thompson 
Reply-To: Freesurfer support list 
Date: Wednesday, August 5, 2015 4:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface reconstruction and quality control





Thanks Martin, I will exclude this subject from my analyses.


On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter 
 wrote:

Hi Emma,

I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here:
http://dx.doi.org/10.1016/j.neuroimage.2014.12.006
http://reuter.mit.edu/papers/reuter-motion14.pdf

Best, Martin


On 08/05/2015 02:55 PM, Emma Thompson wrote:




Hi Freesurfers,

I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see
 that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks
 for you help!

 

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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu 


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Re: [Freesurfer] Total intracranial volumes

[Harms, Michael]

Hi Martin,
Yes, I agree they are different.  Personally, using brain size just makes
more sense to me.  If the point is to show that volume differences are
*beyond* those accounted for by whole brain atrophy, then brain size is
what one would want to use.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/30/15 6:16 PM, "Martin Reuter"  wrote:

Hi Michael and Andre,

Note that controlling for brain size is a totally different thing than
controlling for head size (ICV)!
Brain size shrinks with age and disease severity (even when including
ventricles) and head size stays the same.

E.g. looking at Hippocampus size , controlling for brain size, means you
are interested in testing if the hippocampus is relative small for
someone with that brain size. While the brain size is affected by both
head size and disease.

Cheers, Martin



On 07/30/2015 11:58 AM, Harms, Michael wrote:
> Sure, that would be one option.  Depends on *exactly* what you want to
> include in your covariate.  e.g,. if you wanted the ventricles included,
> you could use SupraTentorial volume instead.
>
> See this wiki page for a description of the various measures in the
> aseg.stats
> http://freesurfer.net/fswiki/MorphometryStats
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 7/30/15 10:32 AM, "Son, Andre"  wrote:
>
> MH,
> Thank you for your suggestion. When you mean whoel brain size, do you
>mean
> the sum of the TotalGrayVol and Total cortical white matter? B/c I don't
> see a parameter called "whole brain size" in my aseg.stats file
>
> Thanks!
> AS
>
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Harms, Michael
> [mha...@wustl.edu]
> Sent: Thursday, July 30, 2015 11:23 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Total intracranial volumes
>
> As an add-on to this, since the ICV (eTIV) is based solely on the
> "talairach transform", you should really QC the accuracy of the talairach
> transform itself if you intend to use ICV as a covariate.  In particular,
> the talairach transform can be off, and thus your estimated ICV would be
> wrong, but the surfaces and aseg may appear just fine.
>
> For this reason, I don't use FS's ICV as a covariate, since it is just
> another thing that would need to be QC'ed.  Rather, I use a estimate of
> whole brain size based on the actual surfaces and segmentation, of which
> you can find a couple options in the top of the aseg.stats file.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 7/30/15 10:12 AM, "Douglas N Greve"  wrote:
>
> The ICV is not estimated from everything under the dura. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV for how we do it
>
> On 07/30/2015 11:08 AM, Son, Andre wrote:
>> Hi Bruce,
>> So if the pial surface was overestimated due to a bad skull strip or
>> because it included a portion of dura and those images were edited and
>> resurfaced, the ICV would not be affected by having the dura and CSF
>> removed in the resurfacing process? That's great!
>>
>> Just to clarify and be sure: ICV = everything under the dura essentially
> >from superior tip of brain to the inferior tip of the cerebellum? CSF,
>> vessels, parenchyma, ventricles. Right?
>>
>> I've seen papers that use ICV for both, I'll explore both methods.
>>
>> Thank you!
>> Andre Son
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, July 30, 2015 11:02 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Total intracranial volumes
>&

Re: [Freesurfer] Total intracranial volumes

[Harms, Michael]

Sure, that would be one option.  Depends on *exactly* what you want to
include in your covariate.  e.g,. if you wanted the ventricles included,
you could use SupraTentorial volume instead.

See this wiki page for a description of the various measures in the
aseg.stats
http://freesurfer.net/fswiki/MorphometryStats

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/30/15 10:32 AM, "Son, Andre"  wrote:

MH,
Thank you for your suggestion. When you mean whoel brain size, do you mean
the sum of the TotalGrayVol and Total cortical white matter? B/c I don't
see a parameter called "whole brain size" in my aseg.stats file

Thanks!
AS


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Harms, Michael
[mha...@wustl.edu]
Sent: Thursday, July 30, 2015 11:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Total intracranial volumes

As an add-on to this, since the ICV (eTIV) is based solely on the
"talairach transform", you should really QC the accuracy of the talairach
transform itself if you intend to use ICV as a covariate.  In particular,
the talairach transform can be off, and thus your estimated ICV would be
wrong, but the surfaces and aseg may appear just fine.

For this reason, I don't use FS's ICV as a covariate, since it is just
another thing that would need to be QC'ed.  Rather, I use a estimate of
whole brain size based on the actual surfaces and segmentation, of which
you can find a couple options in the top of the aseg.stats file.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/30/15 10:12 AM, "Douglas N Greve"  wrote:

The ICV is not estimated from everything under the dura. See
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV for how we do it

On 07/30/2015 11:08 AM, Son, Andre wrote:
> Hi Bruce,
> So if the pial surface was overestimated due to a bad skull strip or
>because it included a portion of dura and those images were edited and
>resurfaced, the ICV would not be affected by having the dura and CSF
>removed in the resurfacing process? That's great!
>
> Just to clarify and be sure: ICV = everything under the dura essentially
>from superior tip of brain to the inferior tip of the cerebellum? CSF,
>vessels, parenchyma, ventricles. Right?
>
> I've seen papers that use ICV for both, I'll explore both methods.
>
> Thank you!
> Andre Son
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>[fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 11:02 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Total intracranial volumes
>
> Hi Andre
>
> why would changing the surfaces affect ICV? We estimate ICV using Randy
> Buckner's method of looking at the determinant of the Talairach
>transform,
> which is totally insensitive to the surface placement.
>
> cheers
> Bruce
>
> p.s. I think it's more common to include ICV as a regression factor than
>to
> directly use percentage, but perhaps someone can comment on this
>
> On Thu, 30 Jul 2015, Son, Andre
> wrote:
>
>> Hello,
>>
>>
>>
>> I'm doing a study comparing subcortical volumes and cortical
>>thicknesses between
>> groups and was planning on normalizing by patients' total intracranial
>>volumes
>> (ICV) as multiple papers have suggested doing.
>>
>>
>>
>> However, many of the scans that Freesurfer analyzed would either
>>overestimate or
>> underestimate the pial and WM surfaces and required manual editing.
>>Once those
>> files were resurfaced, it would in essence change the ICV value,
>>wouldn't it? If
>> that's the case, then are all the literature that used ICV as a
>>normalizing
>> factor potentially using invalid data (b/c I assume many will require
>>the manual
>> edits). These papers also did not elucidate whether or not ICV on its
>>own was
>> significantly different b/w populations, which means the normalization
>>effort may
>> atler the results.
>>
>>
>>
>> Please help. Is there something inhere

Re: [Freesurfer] Total intracranial volumes

[Harms, Michael]

As an add-on to this, since the ICV (eTIV) is based solely on the
"talairach transform", you should really QC the accuracy of the talairach
transform itself if you intend to use ICV as a covariate.  In particular,
the talairach transform can be off, and thus your estimated ICV would be
wrong, but the surfaces and aseg may appear just fine.

For this reason, I don't use FS's ICV as a covariate, since it is just
another thing that would need to be QC'ed.  Rather, I use a estimate of
whole brain size based on the actual surfaces and segmentation, of which
you can find a couple options in the top of the aseg.stats file.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/30/15 10:12 AM, "Douglas N Greve"  wrote:

The ICV is not estimated from everything under the dura. See
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV for how we do it

On 07/30/2015 11:08 AM, Son, Andre wrote:
> Hi Bruce,
> So if the pial surface was overestimated due to a bad skull strip or
>because it included a portion of dura and those images were edited and
>resurfaced, the ICV would not be affected by having the dura and CSF
>removed in the resurfacing process? That's great!
>
> Just to clarify and be sure: ICV = everything under the dura essentially
>from superior tip of brain to the inferior tip of the cerebellum? CSF,
>vessels, parenchyma, ventricles. Right?
>
> I've seen papers that use ICV for both, I'll explore both methods.
>
> Thank you!
> Andre Son
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>[fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 11:02 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Total intracranial volumes
>
> Hi Andre
>
> why would changing the surfaces affect ICV? We estimate ICV using Randy
> Buckner's method of looking at the determinant of the Talairach
>transform,
> which is totally insensitive to the surface placement.
>
> cheers
> Bruce
>
> p.s. I think it's more common to include ICV as a regression factor than
>to
> directly use percentage, but perhaps someone can comment on this
>
> On Thu, 30 Jul 2015, Son, Andre
> wrote:
>
>> Hello,
>>
>>
>>
>> I'm doing a study comparing subcortical volumes and cortical
>>thicknesses between
>> groups and was planning on normalizing by patients' total intracranial
>>volumes
>> (ICV) as multiple papers have suggested doing.
>>
>>
>>
>> However, many of the scans that Freesurfer analyzed would either
>>overestimate or
>> underestimate the pial and WM surfaces and required manual editing.
>>Once those
>> files were resurfaced, it would in essence change the ICV value,
>>wouldn't it? If
>> that's the case, then are all the literature that used ICV as a
>>normalizing
>> factor potentially using invalid data (b/c I assume many will require
>>the manual
>> edits). These papers also did not elucidate whether or not ICV on its
>>own was
>> significantly different b/w populations, which means the normalization
>>effort may
>> atler the results.
>>
>>
>>
>> Please help. Is there something inherent in the software that protects
>>against
>> this issue? Is it still safe to use ICV? And are others not reporting
>>differences
>> b/w ICVs because it is not important or required?
>>
>>
>>
>> Thank you so much.
>>
>> -Andre
>>
>>
>> 
>> This email message, including any attachments, is for the sole use of
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>>
>>
> 
> This email message, including any attachments, is for the sole use of
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>any vir

Re: [Freesurfer] Supratentorial Volume Versus Sum of Parts

[Harms, Michael]

Hi Chris,
I would generate some scatterplots of some of the various "summary" type measures available in aseg.stats.  That will quickly show you if you indeed have some pronounced outliers that don't fall near the regression line.


e.g., compute a 4 x 4 panel scatterplot of CortexVol, SubCortGrayVol, SupraTentorialVol, and SupraTentorialVolNotVent each against each other.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Christopher Owen 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Tuesday, July 14, 2015 9:46 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Supratentorial Volume Versus Sum of Parts






Hello,


We're trying to make multiple comparisons between FreeSurfer outputs on severely atrophied brains and controls. Some of the comparisons are regions of interest, like hippocampal volume
 or the volumes of regions in the frontal lobe, but we've also been making comparisons with supratentorialnotvent or supratentorial. Often, the comparisons are consistant - if all the ROIs we're looking at are small then the whole brain volume (supratentorialnotvent)
 will be significantly smaller as well. 



However, there are some cases where the individual regions in the brain do look smaller than the normal cohort, but the supratentorialnotvent looks about average. This makes sense
 if only a few regions are atrophied, but we've had a few cases where the whole brain is definitely atrophied and the FS assessor definitely looks like it's that way while segmenting the brain, but the supratentorialnotvent volume still looks average. Statistically,
 the ROI's we're interested in for these cases are two standard deviations below the mean for their age, while the stnv is still about average. When looking through the regions FS has available for us that aren't specific
 regions we're interested in, they still all look low. 



How can we explain or understand these situations? It seems like the parts should be close to or equivalent with the whole. 


Thanks,
Washington University in Saint Louis Medical School

Radiology Research Assistant
Christopher Owen









 



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Re: [Freesurfer] couple TRACULA questions

[Harms, Michael]

Hi Anastasia,
Will the next version of TRACULA support the use of 'topup' and 'eddy' by
any chance?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/6/15 12:00 PM, "Anastasia Yendiki" 
wrote:


Forgot to reply re: merging. You have to merge them yourselves, sorry.

On Mon, 6 Jul 2015, Harms, Michael wrote:

>
> Hi Anastasia,
> We are looking at running TRACULA on some data, where we were attracted
>by the longitudinal component of TRACULA.  Is a paper on the longitudinal
> aspect of TRACULA in the works?
>
> If we have multiple dMRI runs/series per imaging session, do we need to
>merge/concatenate those ourselves prior to running trac-all?  (e.g., I
> didn't see anything in the dmrirc config file that would allow one to
>provide multiple DICOM directories per subjlist/baselist entry).
>
> Also, I'm trying to get an initial sense of how much work it is going to
>entail to get this working in our cluster.  In that regard, how customized
> are bedpostx_mgh and fsl_sub_mgh to the MGH cluster?  Could we just
>modify trac-all to use the default bedpostx that comes with FSL 5.0.8,
>and then
> just modify fsl_sub to work in our cluster environment?
>
> thanks!
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
>
>
>
>
>__
>_
>
>
> The materials in this message are private and may contain Protected
>Healthcare Information or other information of a sensitive nature. If you
>are
> not the intended recipient, be advised that any unauthorized use,
>disclosure, copying or the taking of any action in reliance on the
>contents of
> this information is strictly prohibited. If you have received this email
>in error, please immediately notify the sender via telephone or return
> mail.
>
>



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[Freesurfer] couple TRACULA questions

[Harms, Michael]

Hi Anastasia,

We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA.  Is a paper on the longitudinal aspect of TRACULA in the works?



If we have multiple dMRI runs/series
per imaging session, do we need to merge/concatenate those ourselves prior to running
trac-all?  (e.g., I didn't see anything in the dmrirc config file that would allow one to provide multiple DICOM directories per subjlist/baselist
 entry).


Also, I'm trying to get an initial sense of how much work it is going to entail to get this working in our cluster.  In that regard, how customized are
bedpostx_mgh and
fsl_sub_mgh to the MGH cluster?  Could we just modify trac-all to use the default bedpostx that comes with FSL 5.0.8, and then just modify fsl_sub to work in our cluster environment?



thanks!

-MH





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






 



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Re: [Freesurfer] Release of FS version 6.0

[Harms, Michael]

Your analogy just has to be interpreted in the context of the winter of
1936-1937 or more recently 2011-2012, not 2014-2015!
http://www.erh.noaa.gov/box/climate/bossnw.shtml

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/2/15 7:30 AM, "Bruce Fischl"  wrote:

p.s. in case the irony didn't come through on this post, the many levels
and weeks of unit/system/regression testing is an almost completely
unfunded mandate.

On Tue, 2 Jun 2015, Bruce Fischl
wrote:

> Hi Jurgen
>
> we have been working like crazy on it, but it takes huge amounts of time.
> We run through every test then visually inspect the results and if we
>find
> anything wrong no matter how small, we have to fix it and run them all
>again.
> Of course the upside is that the NIH throws money at us like snow in a
>Boston
> winter to do this kind of thing
>
> cheers
> Bruce
>
>
> On Tue, 2 Jun 2015, Jürgen Hänggi wrote:
>
>>  Dear FS experts
>>
>>  I would like to know whether the about date of the FS 6.0 release is
>>  already
>>  known.
>>
>>  Thanks in advance
>>  Best regards
>>  Jürgen Hänggi
>>
>>
>>
>>
>>-
>>--
>>  Jürgen Hänggi, Ph.D.
>>
>>  Division Neuropsychology
>>
>>  Institute of Psychology
>>
>>  University of Zurich
>>
>>  Binzmuehlestrasse 14, PO Box 25
>>
>>  8050 Zurich, Switzerland
>>
>>  0041 44 635 73 97 (phone office)
>>
>>  0041 76 445 86 84 (phone mobile)
>>
>>  0041 44 635 74 09 (fax office)
>>
>>  BIN 4.D.04 (office room number)
>>
>>  j.haenggi[at]psychologie.uzh.ch (email)
>>
>>  http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>>  http://www.juergenhaenggi.ch (private website)
>>
>>
>>  This e-mail (and any attachment/s) contains confidential
>>
>>  and/or privileged information. If you are not the intended
>>
>>  recipient (or have received this e-mail in error) please notify
>>
>>  the sender immediately and destroy this e-mail. Any
>>
>>  unauthorised copying, disclosure or distribution of the
>>
>>  material in this e-mail is strictly forbidden.
>>
>>
>>-
>>--
>>
>>
>>
>>



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Re: [Freesurfer] crossing medial surfaces

[Harms, Michael]

Not that I recall.  Sorry for conflating a different issue.

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/24/15 8:22 AM, "Bruce Fischl"  wrote:

Hi Mike

yes, I remember that and it is fixed in the upcoming 6.0. Not sure if
that handles crossing the midline though. Were you having that issue, or
just white/pial crossing?

cheers
Bruce
On Fri, 24 Apr 2015, Harms, Michael wrote:

>
> Is this perhaps the same issue that I reported in this thread?:
>
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html
>
> If so, it is due to a "bug" of sort in the recon-all in v5.3
>
> It appears that some of our followup conversation occurred off list, so
> for others benefit, I'm pasting in the key exchange below (and to remind
> Bruce):
>
> --- from Bruce ---
> ok, I see what's going on. Here is the sequence of calls:
>
> 1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
> L408_base lh
>
> Makes the white surface *without* using the aparc. Because there are a
> string of "hypointensity" labels in the aseg, the white surface is frozen
> in these locations.
>
> 2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
> lh
>
> internally recreates the white surface but doesn't save it. The frozen
> vertices are allowed to move since the aparc *is* used in this call, and
> the vertices are deemed to be in real cortical regions.
>
> The pial surface then starts from the (inwards deformed but not written
>to
> disk) white surface, and then settles inside the white surface that is on
> disk.
>
> I'm not sure how we settled on this logic. Why recreate the white
>surface?
> Why not run with -nowhite -orig_pial white? That way the algorithm uses
>the
> white surface that the user can see and things should be consistent
>
> Bruce
>
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.   Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 4/24/15 7:42 AM, "Bruce Fischl"  wrote:
>
> no, I don't think it would. If you upload a case with crossing surfaces
> I'll take a look
> cheers
> Bruce
> On Fri, 24 Apr 2015, Clara Kuehn wrote:
>
>> Dear Bruce,
>> thanks for the reply. I often have the case that the aseg.mgz is already
>> correct, however the surfaces cross because the aparc+aseg.mgz
>> incorrectly classified the hemispheres. If running autorecon2-cp uses
>>the
>> aseg.mgz, which is already correct, would that make any changes to the
>> aparc+aseg.mgz?
>>
>> Cheers, Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Bruce Fischl" 
>> An: "Freesurfer support list" 
>> Gesendet: Freitag, 24. April 2015 03:12:55
>> Betreff: Re: [Freesurfer] crossing medial surfaces
>>
>> I don't think you want noaseg. Why not try autorecon2-cp so it starts
>> after the aseg but uses it?
>>
>> cheers
>> Bruce
>> On Thu, 23 Apr 2015, Clara Kuehn wrote:
>>
>>> Hi Paul,
>>>
>>> thanks for your reply. I think the problem is that after editing the
>>> aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the
>>> aparc+aseg.mgz, so the surfaces still cross.
>>>
>>> Cheers, Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: silve...@gmx.com
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Donnerstag, 23. April 2015 03:24:51
>>> Betreff: Re: [Freesurfer] crossing medial surfaces
>>>
>>> Hi Clara,
>>> The method for dealing with the crossing medial surfaces that works for
>>> me is decribed in the email below. Though, I'm not sure if there are
>>>any
>>> issues or concerns with this approach particularly in regard to
>>> thickness or the segmentations.
>>> Paul
>>> Sent: Tuesday, October 22, 2013 at 9:49 AM
>>> From: "silve...@gmx.com" 
>>> To: "Bruce Fischl" 
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] medial wall crossing the surface: repost
>>>

Re: [Freesurfer] crossing medial surfaces

[Harms, Michael]

Is this perhaps the same issue that I reported in this thread?:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html

If so, it is due to a "bug" of sort in the recon-all in v5.3

It appears that some of our followup conversation occurred off list, so
for others benefit, I'm pasting in the key exchange below (and to remind
Bruce):

--- from Bruce ---
ok, I see what's going on. Here is the sequence of calls:

1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh

Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.

2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh

internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.

The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.

I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses the
white surface that the user can see and things should be consistent

Bruce


--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/24/15 7:42 AM, "Bruce Fischl"  wrote:

no, I don't think it would. If you upload a case with crossing surfaces
I'll take a look
cheers
Bruce
On Fri, 24 Apr 2015, Clara Kuehn wrote:

> Dear Bruce,
> thanks for the reply. I often have the case that the aseg.mgz is already
>correct, however the surfaces cross because the aparc+aseg.mgz
>incorrectly classified the hemispheres. If running autorecon2-cp uses the
>aseg.mgz, which is already correct, would that make any changes to the
>aparc+aseg.mgz?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" 
> An: "Freesurfer support list" 
> Gesendet: Freitag, 24. April 2015 03:12:55
> Betreff: Re: [Freesurfer] crossing medial surfaces
>
> I don't think you want noaseg. Why not try autorecon2-cp so it starts
> after the aseg but uses it?
>
> cheers
> Bruce
> On Thu, 23 Apr 2015, Clara Kuehn wrote:
>
>> Hi Paul,
>>
>> thanks for your reply. I think the problem is that after editing the
>>aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the
>>aparc+aseg.mgz, so the surfaces still cross.
>>
>> Cheers, Clara
>>
>> - Ursprüngliche Mail -
>> Von: silve...@gmx.com
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Donnerstag, 23. April 2015 03:24:51
>> Betreff: Re: [Freesurfer] crossing medial surfaces
>>
>> Hi Clara,
>> The method for dealing with the crossing medial surfaces that works for
>>me is decribed in the email below. Though, I'm not sure if there are any
>>issues or concerns with this approach particularly in regard to
>>thickness or the segmentations.
>> Paul
>> Sent: Tuesday, October 22, 2013 at 9:49 AM
>> From: "silve...@gmx.com" 
>> To: "Bruce Fischl" 
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] medial wall crossing the surface: repost
>> Thanks Bruce for your response, I'll fix aseg where it is incorrect,
>>but what about the instances where the aseg is correct and the pial
>>surfaces cross? Other than needing to update aseg.stats, are there any
>>other concerns with the 'hemisphere' approach I described below?
>>
>> Thanks again,
>> Paul
>>
>>
>>
>>> - Original Message -
>>> From: Bruce Fischl
>>> Sent: 10/22/13 09:46 AM
>>> To: silve...@gmx.com
>>> Subject: Re: [Freesurfer] medial wall crossing the surface: repost
>>>
>>> Try fixing the aseg and rerunning
>>> Cheers
>>> Bruce
>>>
 On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" 
wrote:

 Not always, but yes, in some instances the aseg crosses.


> - Original Message -
> From: Bruce Fischl
> Sent: 10/18/13 01:22 PM
> To: silve...@gmx.com
> Subject: Re: [Freesurfer] medial wall crossing the surface
>
> Does the aseg cross as well?
>
>
>
>> On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" 
>>wrote:
>>
>> Dear All,
>>
>> I too am seeing the medial pial surfaces crossing hemispheres in
>>some subjects.
>>
>> The approach that appears to be working for me involves making
>>copies of brainmask.mgz and aseg.mgz
>> For the left hemisphere crossing into the right, edit brainmask.mgz
>>and aseg.mgz to delete voxels at the crossing belonging to the right
>>hemisphere.
>> I then run recon-all -autorecon-pial -hemi lh -subjid subject
>> followed by returning the brainm

Re: [Freesurfer] updating from 5.0 to 5.3

[Harms, Michael]

FreeSurfer will preserve your previous edits (e.g., brainmask.mgz edit, or wm.mgz edits, among others) when you run a newer version on top of an older version.  However, that is no guarantee that there won't be any issues following the re-processing with
 the newer version, so it is best to at least view the data again.  We have certainly seen instances where some additional edits were warranted after updating with a newer version.


You shouldn't have some subjects in a study processed with 5.0 and others with 5.3.  But if all subjects were initially processed with 5.0, and you update all of them with 5.3 (and then re-QC afterwards), that is fine.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Aaron Goldman 
Reply-To: Freesurfer support list 
Date: Wednesday, February 11, 2015 2:22 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] updating from 5.0 to 5.3





Hello,

I have a large set of images previously run in FreeSurfer 5.0. I'm also preparing to run a new batch of images and debating whether to use 5.3 or stick with 5.0. If I updated all the old datasets to 5.3, would I need to visually QC them a second time, or are
 the versions similar enough that I can rely on my pre-existing QC? Also, am I correct in assuming I shouldn't mix versions 5.0 and 5.3?

Thanks,

Aaron






 



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Re: [Freesurfer] Meninges labelled as cortex

[Harms, Michael]

Make sure that you are looking at the surfaces though.  It looks like the
image you attached was the aseg.mgz, and you should not be using the
"cortex" as defined in the aseg.mgz because that is based on the
volume-stream segmentation.  Either overlay the surfaces, or take a look
at the aparc+aseg.mgz instead to see if you really have dura included
within the pial surface.  (The aparc+aseg.mgz uses the pial surface to
"mask out" any cortex in the aseg.mgz that was outside the pial surface).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/7/15 9:12 AM, "Bruce Fischl"  wrote:

>Hi Amanda
>
>it depends what you are doing. They will certainly distort thickness
>estimates in those regions. It is really, really hard to get rid of dura
>unless you acquire data for that purpose. If you have a highres FLAIR or
>T2
>or a multi-echo mprage we have tools for automatically avoiding it.
>
>cheers
>Bruce
>
>
>On Wed, 7 Jan 2015, Worker, Amanda wrote:
>
>>
>> Hi All,
>>
>>
>> I have noticed that almost all of my data has some voxels of dura that
>>have
>> incorrectly been labelled as cortex. It doesn't look like a severe
>>problem
>> and I've attached a screen shot to show you.
>>
>>
>> I'm just wondering whether this is something that will affect my
>>results? I
>> have tried using -gcut and adjusting the watershed parameters to a
>>height of
>> 24, but nothing seems to work. As I have many subjects it would be very
>>time
>> consuming to manually adjust all of these voxels.
>>
>>
>> Do you think this poses a problem or can I leave it as it is?
>>
>>
>> Best wishes,
>>
>>
>> Amanda
>>
>>



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[Freesurfer] display thickness map in freeview

[Harms, Michael]

Hi,
How does one go about loading a thickness map within freeview?
The OutputData_freeview tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview)
contains a long command line example, but I can't figure out how one would accomplish the same just within the GUI.  (Sorry if I'm missing that info elsewhere).


Once you have a surface loaded (e.g., inflated, pial), I'd think that you would want to use the "Overlay" section of the freeview menu for that surface, but both the "Load generic" and "Load correlation" options prompt me to select a volume file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



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Re: [Freesurfer] pial surface crossing white

[Harms, Michael]

Yeah, the time stamps look fine, and the euler numbers are correct.
I've uploaded the pre-edited (L408_base_orig.tgz) and edited (L408_base.tgz) directories.


This was related to the creation of a 'base' template, so the commands are a little bit involved. 


For the "L408_base_orig" set of data:

recon-all -base L408_base -tp L408_110502 -tp L408_120817 -tp L408_130819 -all -mprage -expert expert.opts



For the edits in "L408_base":

recon-all -base L408_base -tp L408_110502 -tp L408_120817 -tp L408_130819 -autorecon2-wm -autorecon3 -mprage



Hopefully you can investigate without needing the "cross" time points, but if you need those, I could ftp those as well.


thanks,
-MH


-- 
Michael Harms, Ph.D.


---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO  63110
Email: mha...@wustl.edu







On 9/29/14 8:49 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:



Hi Mike


that's really strange. Are you sure you recreated the pial??? Can you 
double check time-stamps and such? And Euler number to make sure that it is 
the same for white and pial? If that all looks right, upload the subject 
and send me the command line you used for the rerunning and I'll 
investigate.


cheers
Bruce




On Wed, 24 Sep 2014, Harms, Michael wrote:




Hi,
We are seeing some instances where the pial surface is crossing over the white surface in the vicinity of the precuneus and
lingual cortex, where there is only a thin strand of WM separating the GM from the lateral ventricle.  In these cases, it
appears that GM is getting labeled as "WM-hypointensities" in the aseg, and then assigned a value of 250 in the wm.mgz.  So, we
deleted those erroneous values in the wm.mgz (changing them from 250 to 1).  The resulting white surfaces following these edits
are a much better reflection of where the white surface should be, but the pial surface still crosses over into the WM.  See
attached png's for examples in two subject, where there are both "PreWMedit" and "PostWMedit" snapshots for each of the two
subjects.  (In each of the attached examples, the issue is on the left hemi -- i.e,. right side of the snapshot).

My question is:  Is there some other way that we are supposed to edit this?  Or, having fixed the gross errors in the white
surface, do we just have to accept the remaining inaccuracy in the pial surface.  It's a fairly localized remaining error in the
pial surface, but I'm puzzled how it ends up on the wrong side of the white surface to begin with.

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

 





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immediately notify the sender via telephone or return mail.









 



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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

[Harms, Michael]

The pipelines documentation should include fairly extensive documentation to get you going.
If you have further questions, you should switch over to using the HCP-Users list.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 19, 2014 10:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion








Thank you Michael for this link !


However, it seems that we have to install very precise versions of FSL and Freesurfer.


Once we get fsl-5.0.6 package (http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this one and which wiki to follow ?


Cheers,








-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France




2014-09-19 16:35 GMT+02:00 Harms, Michael 
<mha...@wustl.edu>:





Hi,
I suggest you start with the documentation that accompanies the recently released HCP pipelines.
see
http://www.humanconnectome.org/documentation/HCP-pipelines/
and the link therein to the pipelines on GitHub.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 19, 2014 9:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion











Dear Freesurfer's experts,


I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.


The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).


I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage (https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping)
 with no download link...


Where can I find this package and how to use it ?


Many thanks !


Best,










-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France

















 



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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

[Harms, Michael]

Hi,
I suggest you start with the documentation that accompanies the recently released HCP pipelines.
see
http://www.humanconnectome.org/documentation/HCP-pipelines/
and the link therein to the pipelines on GitHub.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Matthieu Vanhoutte 
Reply-To: Freesurfer support list 
Date: Friday, September 19, 2014 9:23 AM
To: Freesurfer support list 
Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion









Dear Freesurfer's experts,


I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.


The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).


I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage (https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping)
 with no download link...


Where can I find this package and how to use it ?


Many thanks !


Best,










-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France















 



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Re: [Freesurfer] quick quality assessment for MPRAGE images

[Harms, Michael]

Yes, that can be helpful.  As a caution though, the overall quality may appear fine, but things like topology correction errors can still occur and will be quite local.  Thus, they would easily be missed if the density of your screenshots isn't high enough.
  Personally, I find it only marginally more time consuming to navigate through the entire set of slices in 'tkmedit', and the quality of your QA will be better.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Chris Watson <christopher.wat...@childrens.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 18, 2014 2:00 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] quick quality assessment for MPRAGE images




Try out Freesurfer's QAtools. It still isn't "automatic", but you can get a bunch of screenshots and view them all on an html page.


On 09/18/2014 11:42 AM, Harms, Michael wrote:





Hi Ezra,
I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion.  It is time consuming, but you have to put eyes on the
 data.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: , Ezra <ezra_wegbr...@brown.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 18, 2014 9:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] quick quality assessment for MPRAGE images






Dear Freesurfer Users,


I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values.  However, some of the MPRAGE scans are
 contaminated by subject motion, but the extent of this varies from scan to scan.   Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?  


Thanks!
Ezra


___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital 
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org                                  
                                                                                         
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Re: [Freesurfer] quick quality assessment for MPRAGE images

[Harms, Michael]

Hi Ezra,
I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion.  It is time consuming, but you have to put eyes on the
 data.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: , Ezra 
Reply-To: Freesurfer support list 
Date: Thursday, September 18, 2014 9:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] quick quality assessment for MPRAGE images






Dear Freesurfer Users,


I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values.  However, some of the MPRAGE scans are
 contaminated by subject motion, but the extent of this varies from scan to scan.   Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?  


Thanks!
Ezra


___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital 
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org                                                          
                                                                 
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Re: [Freesurfer] how to shrink wm surface

[Harms, Michael]

Hi Bruce,
I was wondering if there is info somewhere about what each of those 7 MIN_
and MAX_ variables control regarding the positioning of the white and pial
surfaces?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 9/9/14 7:35 AM, "Bruce Fischl"  wrote:

>Hi Andrea
>
>what is the background image? This is usually either a failure of the
>intensity normalization or of the surface deformation/segmentation to
>adaptively estimate the underlying intensity distributions of the
>gray/white matter. If you look in recon-all.log for that subject you will
>find a set of lines like:
>
>setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
>setting MAX_BORDER_WHITE to 112.0 (was 105)
>setting MIN_BORDER_WHITE to 83.0 (was 85)
>setting MAX_CSF to 59.1 (was 40)
>setting MAX_GRAY to 100.0 (was 95)
>setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75)
>setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40)
>
>
>
>in your case for example you will probably find that the min_border_white
>is too high or tha the max_gray is too low. You can set these using the
>expert opts for both mri_segment and mris_make_surfaces.
>
>cheers
>Bruce
>
>
>On Tue, 9 Sep 2014, Andrea
>Horváth wrote:
>
>> Dear Freesurfers,
>>
>>
>> After running recon-all, the wm surfaces are too close to the pial
>>surface,
>> some gray matter is segmented as white matter as seen in the attached
>> picture (red cross: a bigger cortical part is included in the white
>>matter).
>>
>> How can I shrink the wm surface?
>>
>> Thank you for your help!
>>
>> Andrea
>>
>>
>>
>>
>>
>>
>>



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Re: [Freesurfer] Cortical Thickness Correction Factor

[Harms, Michael]

How many subjects are in each group, and how large is the "subsample" of patients which you scanned on both scanner on the same day?  The issue at hand is whether that subsample is large enough to get an accurate and meaningful estimate of the "scanner"
 effect to use as a covariate.  Unless that subsample is reasonably large, you are stuck with a situation where "scanner" is rather hopelessly confounded with "group".  


Stated differently, as you know, you ideally want scanner and group to be orthogonal (i.e., balanced design).  Depending on the N of the subsample, I suspect that they are probably actually highly co-linear in your case, which means that inclusion of a
 scanner covariate is probably going to account for most of whatever variability you have that may be an actual group effect (if one exists), which means that your odds of seeing any group difference are rather low.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Chris Watson 
Reply-To: Freesurfer support list 
Date: Friday, August 8, 2014 1:21 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Cortical Thickness Correction Factor




In your FSGD you'll have to add a covariate for "scanner"


On 08/08/2014 12:34 PM, David Tate wrote:

FreeSurfer Gurus,


I would like to pose this question again to the group if possible.  We are working with data that comes from two different scanners.  Our experimental group was collected on one scanner and then control data was acquired on another scanner.  Not the optimal
 situation I realize but unavoidable.  We were fortunate to be able to acquire imaging for a subsample of patients on both scanners in the same day.  Preliminary results suggest that one site measures cortical thickness and subcortical volumes in a non-significant
 (statistically) but consistent direction with one scanner producing larger volume and thickness measures.  




My question is whether or not it is possible to mathematically account for these differences in any analysis that we are doing using FreeSurfer and if so where can I find those procedures for practically implementing the correction?




Thanks in advance for any help with this.




David






On Apr 17, 2014, at 11:07 AM, David Tate  wrote:



We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites).


Is it possible to include a correction factor adjusting for the scanner differences when using glmfit or qdec?


Thanks,


David




David F. Tate, Ph.D.

Research Neuropsychologist

Defense and Veterans Brain Injury Center
Contractor, General Dynamics Information Technology
Brooke Army Medical Center MCHE MDU (DVBIC)
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Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Hi,
In response to Christophe's question, I looked at the two other whole
brain parcellation schemes -- DKTatlas40 and a2009s.  In those two
subjects at least, that medial region which is labelled "insula" in the
aparc.annot is labelled (mostly) as medial/lateral orbitofrontal (with
some even as rostralanteriorcingulate) in aparc.DKTatlas40.annot, and as
G_subcallosal in aparc.a2009s.annot.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/8/14 10:30 AM, "Harms, Michael"  wrote:

>
>Hi Christophe,
>I uploaded both subjects that I showed the snapshots for yesterday into
>the FS FTP drop site.  (Do you have access to that?)
>
>cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.  Tel: 314-747-6173
>St. Louis, MO  63110   Email: mha...@wustl.edu
>
>
>
>
>On 8/7/14 4:03 PM, "Christophe Destrieux"
> wrote:
>
>>Hi Michael
>>the limen insula explanation sounds ok, even if it's extension on the
>>medial surface seem really large. would you have a snapshot to look on
>>the volume to which structure this label anatomically corresponds to ?
>>Also did you had a look to the results of the insula aparc with the 2009a
>>atlas?
>>cd
>>
>>--
>>Christophe Destrieux,
>>
>>Directeur du Département Communication et Multimédia
>>http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651
>>1
>>59612
>>
>>Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François
>>Rabelais de Tours
>>http://www.u930.tours.inserm.fr/
>>
>>Service de Neurochirurgie
>>et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
>>37032 Tours - France
>>tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
>>
>>
>>- Mail original -
>>De: "Michael Harms" 
>>À: "Freesurfer support list" 
>>Cc: "Ron KILLIANY" 
>>Envoyé: Jeudi 7 Août 2014 22:18:49
>>Objet: Re: [Freesurfer] insula on medial surface
>>
>>
>>I'm not itching to re-process this data so I like that explanation as
>>well.  I think my main concern is that that bit of insula label seems
>>somewhat arbitrary and inconsistent, in that some subjects have this bit
>>of medial tissue labelled as insula, whereas others don't.  (Even within
>>the same subject, it isn't consistent between the two hemispheres).
>>
>>I guess it is just a matter of the sulcal variability and atlas labeling
>>resulting in variability in that particular region.  Presumably, Ron must
>>have labelled that bit of tissue as "insula" in some subjects, but not
>>others??
>>
>>Ron: It would be great to hear what kind of "rule" you applied when
>>labeling the individual subjects in the atlas in that particular region
>>when deciding whether it should be considered insula or medial/lateral
>>orbitofrontal.
>>
>>thanks,
>>-MH
>>
>>--
>>Michael Harms, Ph.D.
>>
>>---
>>Conte Center for the Neuroscience of Mental Disorders
>>Washington University School of Medicine
>>Department of Psychiatry, Box 8134
>>660 South Euclid Ave.   Tel: 314-747-6173
>>St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>>On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:
>>
>>>wow, I like that answer much more than "it's a bug"! Can we go with
>>>Paul's explanation?
>>>
>>>
>>>Bruce
>>>
>>>On Thu, 7 Aug 2014, Paul Beach wrote:
>>>
>>>> I asked a neuroanatomist and insula expert on my campus about this a
>>>>while
>>>> back and this was his response:
>>>> "This is the region of the "limen insulae" that you will remember Dr.
>>>>Heimer
>>>> referring to often in the brain dissection course. The insula is
>>>>defined as
>>>> cortex which is covered by a lid of other cortical lobes, frontal,
>>>>parietal
>>>> a

Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Hi Christophe,
I uploaded both subjects that I showed the snapshots for yesterday into
the FS FTP drop site.  (Do you have access to that?)

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/7/14 4:03 PM, "Christophe Destrieux"
 wrote:

>Hi Michael
>the limen insula explanation sounds ok, even if it's extension on the
>medial surface seem really large. would you have a snapshot to look on
>the volume to which structure this label anatomically corresponds to ?
>Also did you had a look to the results of the insula aparc with the 2009a
>atlas?
>cd
>
>--
>Christophe Destrieux,
>
>Directeur du Département Communication et Multimédia
>http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=12006511
>59612
>
>Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François
>Rabelais de Tours
>http://www.u930.tours.inserm.fr/
>
>Service de Neurochirurgie
>et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
>37032 Tours - France
>tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
>
>
>- Mail original -
>De: "Michael Harms" 
>À: "Freesurfer support list" 
>Cc: "Ron KILLIANY" 
>Envoyé: Jeudi 7 Août 2014 22:18:49
>Objet: Re: [Freesurfer] insula on medial surface
>
>
>I'm not itching to re-process this data so I like that explanation as
>well.  I think my main concern is that that bit of insula label seems
>somewhat arbitrary and inconsistent, in that some subjects have this bit
>of medial tissue labelled as insula, whereas others don't.  (Even within
>the same subject, it isn't consistent between the two hemispheres).
>
>I guess it is just a matter of the sulcal variability and atlas labeling
>resulting in variability in that particular region.  Presumably, Ron must
>have labelled that bit of tissue as "insula" in some subjects, but not
>others??
>
>Ron: It would be great to hear what kind of "rule" you applied when
>labeling the individual subjects in the atlas in that particular region
>when deciding whether it should be considered insula or medial/lateral
>orbitofrontal.
>
>thanks,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.   Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:
>
>>wow, I like that answer much more than "it's a bug"! Can we go with
>>Paul's explanation?
>>
>>
>>Bruce
>>
>>On Thu, 7 Aug 2014, Paul Beach wrote:
>>
>>> I asked a neuroanatomist and insula expert on my campus about this a
>>>while
>>> back and this was his response:
>>> "This is the region of the "limen insulae" that you will remember Dr.
>>>Heimer
>>> referring to often in the brain dissection course. The insula is
>>>defined as
>>> cortex which is covered by a lid of other cortical lobes, frontal,
>>>parietal
>>> and temporal. They all fold over except at the inferior frontal end
>>>where a
>>> little bit of the surface of otherwise insular cortex is not covered,
>>>and
>>> this little corner peeks out. This is the limeninsula which neighbors
>>>the
>>> olfactory cortex on the inferior surface of the frontal lobe and the
>>>medial
>>> surface of the temporal lobe, and is olfactory cortex itself. Since it
>>>is
>>> not covered over, it technically might not be considered really
>>>"insular"
>>> but it is obviously in continuity with, and not separated by any kind
>>>of
>>> sulcus or other landmark, from the rest of the insular covered cortex.
>>>So we
>>> are left with no secure boundary line between insular cortex and
>>>inferior
>>> frontal and medial temporal cortex in this corner. It looks like
>>>Freesurfer
>>> has decided to call it all insular, and with good functional reasons."
>>>
>>>
>>> Cheers,
>>>
>>>
>>>
>>> On Thu, Aug 7, 2014 at 3:32 PM, Bruce Fischl
>>>
>>> wrote:
&

Re: [Freesurfer] insula on medial surface

[Harms, Michael]

I'm not itching to re-process this data so I like that explanation as
well.  I think my main concern is that that bit of insula label seems
somewhat arbitrary and inconsistent, in that some subjects have this bit
of medial tissue labelled as insula, whereas others don't.  (Even within
the same subject, it isn't consistent between the two hemispheres).

I guess it is just a matter of the sulcal variability and atlas labeling
resulting in variability in that particular region.  Presumably, Ron must
have labelled that bit of tissue as "insula" in some subjects, but not
others??

Ron: It would be great to hear what kind of "rule" you applied when
labeling the individual subjects in the atlas in that particular region
when deciding whether it should be considered insula or medial/lateral
orbitofrontal.

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:

>wow, I like that answer much more than "it's a bug"! Can we go with
>Paul's explanation?
>
>
>Bruce
>
>On Thu, 7 Aug 2014, Paul Beach wrote:
>
>> I asked a neuroanatomist and insula expert on my campus about this a
>>while
>> back and this was his response:
>> "This is the region of the "limen insulae" that you will remember Dr.
>>Heimer
>> referring to often in the brain dissection course. The insula is
>>defined as
>> cortex which is covered by a lid of other cortical lobes, frontal,
>>parietal
>> and temporal. They all fold over except at the inferior frontal end
>>where a
>> little bit of the surface of otherwise insular cortex is not covered,
>>and
>> this little corner peeks out. This is the limeninsula which neighbors
>>the
>> olfactory cortex on the inferior surface of the frontal lobe and the
>>medial
>> surface of the temporal lobe, and is olfactory cortex itself. Since it
>>is
>> not covered over, it technically might not be considered really
>>"insular"
>> but it is obviously in continuity with, and not separated by any kind of
>> sulcus or other landmark, from the rest of the insular covered cortex.
>>So we
>> are left with no secure boundary line between insular cortex and
>>inferior
>> frontal and medial temporal cortex in this corner. It looks like
>>Freesurfer
>> has decided to call it all insular, and with good functional reasons."
>>
>>
>> Cheers,
>>
>>
>>
>> On Thu, Aug 7, 2014 at 3:32 PM, Bruce Fischl
>>
>> wrote:
>>   Hi Mike
>>
>>   I'm not sure - I think the insula was an additional label that
>>   Ron Killiany added. I'll cc Ron to see if he has any insight. It
>>   certainly looks too medial to me.
>>
>>   I would also check on the white surface just to make sure that
>>   it's not a quirk of the inflation. If the aseg looks right we
>>   could certainly put together some simple auto-editing to correct
>>   this kind of thing
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 7 Aug 2014, Harms, Michael wrote:
>>
>>
>>   Hi,
>>   An astute RA, while reviewing the aparc+aseg.mgz of brains
>>   processed with FS
>>   5.3, noticed a fair number of instances, where the insula
>>   label "wraps
>>   around" pretty medially, where she was expecting to see
>>   orbitofrontal as the
>>   label.  See attached jpg's for two examples shown on the
>>   inflated surface.
>>Since this is fairly common, I'm assuming that this isn't
>>   anything to be
>>   concerned about, but just wanted to confirm.
>>
>>   Has this always been the behavior of the insula label, and
>>   we just didn't
>>   notice it previously?
>>
>>   thanks,
>>   -MH
>>
>>   --
>>   Michael Harms, Ph.D.
>>   ---
>>   Conte Center for the Neuroscience of Mental Disorders
>>   Washington University School of Medicine
>>   Department of Psychiatry, Box 8134
>>   660 South Euclid Ave. Tel: 314-747-6173
>>   St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>>
>>
>>
>>

Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Yeah, it is labelled as "Cerebral-cortex" in the aseg.mgz, and is just
medial to the "Accumbens" label.

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/7/14 2:52 PM, "Bruce Fischl"  wrote:

>so that region really is cortex? It's not filled in ventricle or
>anything?
>On Thu, 7 Aug 2014, Harms, Michael wrote:
>
>>
>> Yeah, the insula label is present medially when viewed on the white
>> surface as well, so its not just a quirk of the inflation.
>>
>> Not sure if I follow what you mean by the "aseg looking right".  The
>> aparc+aseg.mgz is actually where the RA first noticed the issue, since
>>she
>> noticed that some of the voxels labeled as insula were wrapping around
>>all
>> the way onto the medial surface.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.   Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 8/7/14 2:32 PM, "Bruce Fischl"  wrote:
>>
>>> Hi Mike
>>>
>>> I'm not sure - I think the insula was an additional label that Ron
>>> Killiany
>>> added. I'll cc Ron to see if he has any insight. It certainly looks too
>>> medial to me.
>>>
>>> I would also check on the white surface just to make sure that it's
>>>not a
>>> quirk of the inflation. If the aseg looks right we could certainly put
>>> together some simple auto-editing to correct this kind of thing
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 7 Aug 2014, Harms, Michael wrote:
>>>
>>>>
>>>> Hi,
>>>> An astute RA, while reviewing the aparc+aseg.mgz of brains processed
>>>> with FS
>>>> 5.3, noticed a fair number of instances, where the insula label "wraps
>>>> around" pretty medially, where she was expecting to see orbitofrontal
>>>> as the
>>>> label.  See attached jpg's for two examples shown on the inflated
>>>> surface.
>>>>  Since this is fairly common, I'm assuming that this isn't anything to
>>>> be
>>>> concerned about, but just wanted to confirm.
>>>>
>>>> Has this always been the behavior of the insula label, and we just
>>>> didn't
>>>> notice it previously?
>>>>
>>>> thanks,
>>>> -MH
>>>>
>>>> --
>>>> Michael Harms, Ph.D.
>>>> ---
>>>> Conte Center for the Neuroscience of Mental Disorders
>>>> Washington University School of Medicine
>>>> Department of Psychiatry, Box 8134
>>>> 660 South Euclid Ave. Tel: 314-747-6173
>>>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>___
>>>>__
>>>> ___
>>>>
>>>>
>>>> The materials in this message are private and may contain Protected
>>>> Healthcare Information or other information of a sensitive nature. If
>>>> you
>>>> are not the intended recipient, be advised that any unauthorized use,
>>>> disclosure, copying or the taking of any action in reliance on the
>>>> contents
>>>> of this information is strictly prohibited. If you have received this
>>>> email
>>>> in error, please immediately notify the sender via telephone or return
>>>> mail.
>>>>
>>>>
>>
>>
>> 
>> The materials in this message are private and may contain Protected
>>Healthcare Information or other information of a sensitive nature. If
>>you are not the intended recipient, be advised that any unauthorized
>>use, disclosure, copying or the taking of any action in reliance on the
>&g

Re: [Freesurfer] insula on medial surface

[Harms, Michael]

Yeah, the insula label is present medially when viewed on the white
surface as well, so its not just a quirk of the inflation.

Not sure if I follow what you mean by the "aseg looking right".  The
aparc+aseg.mgz is actually where the RA first noticed the issue, since she
noticed that some of the voxels labeled as insula were wrapping around all
the way onto the medial surface.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/7/14 2:32 PM, "Bruce Fischl"  wrote:

>Hi Mike
>
>I'm not sure - I think the insula was an additional label that Ron
>Killiany
>added. I'll cc Ron to see if he has any insight. It certainly looks too
>medial to me.
>
>I would also check on the white surface just to make sure that it's not a
>quirk of the inflation. If the aseg looks right we could certainly put
>together some simple auto-editing to correct this kind of thing
>
>cheers
>Bruce
>
>
>On Thu, 7 Aug 2014, Harms, Michael wrote:
>
>>
>> Hi,
>> An astute RA, while reviewing the aparc+aseg.mgz of brains processed
>>with FS
>> 5.3, noticed a fair number of instances, where the insula label "wraps
>> around" pretty medially, where she was expecting to see orbitofrontal
>>as the
>> label.  See attached jpg's for two examples shown on the inflated
>>surface.
>>  Since this is fairly common, I'm assuming that this isn't anything to
>>be
>> concerned about, but just wanted to confirm.
>>
>> Has this always been the behavior of the insula label, and we just
>>didn't
>> notice it previously?
>>
>> thanks,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>>
>>
>>
>>
>>_
>>___
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>>you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the
>>contents
>> of this information is strictly prohibited. If you have received this
>>email
>> in error, please immediately notify the sender via telephone or return
>>mail.
>>
>>



The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] Diffusion analysis qs - gradient matrix

[Harms, Michael]

FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Rotem Saar 
Reply-To: Freesurfer support list 
Date: Monday, July 21, 2014 1:54 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Diffusion analysis qs - gradient matrix






Dear freesurfer experts,


For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects.


The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for
 converting dicoms to nifti) looks different.


This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix.


So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? 


Thanks




Rotem Saar-Ashkenazy


Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105



School of Social Work
Ashkelon Academic College, Ashkelon, 78211 



Israel








 



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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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Re: [Freesurfer] Why the result was not same for the same subject

[Harms, Michael]

Actually, if you run 'recon-all' a second time (from scratch) on the same
subject, on the same platform/architecture, and you use the default
recon-all settings (i.e., don't use the -randomness flag, or specify your
random seed via the -rng-seed flag), then you should get identical
results, because for quite a few versions now, recon-all has been set up
to use the same random seed (1234) in all the binaries that involve
randomness.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/23/14 12:05 PM, "Chiu, Bryan (PHTH)"  wrote:

>There of course is some variability in the analysis due to the way the
>segmentation happens. Your results are certainly not out of the ordinary
>for the volume you are viewing. On average you can expect a ~1% variance
>between several scans of the same subject.
>
>If you want to know more I certainly suggest reading the paper titled:
>"Whole Brain Segmentation: Automated Labeling of Neuroanatomical
>Structures in the Human Brain"
>
>- Bryan
>
>
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
>



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Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

[Harms, Michael]

Hi,
The recon-all based striatal parcellations are based on the anatomy of each particular subject, guided by a probabilistic atlas.  That is inherently likely to be more accurate that just taking a set of ROIs/parcellations defined in some (non-probabilistic)
 atlas and warping them to each subject via an affine transformation, which is what it sounds like you are doing with the "Choi ROIs".


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Paul Beach 
Reply-To: Freesurfer support list 
Date: Wednesday, June 18, 2014 8:52 AM
To: Freesurfer support list 
Cc: Thomas Yeo , "Yeo, Boon Thye Thomas -- Boon Thye Thomas Yeo" 
Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain





Hi Bruce,


Thanks for the response. 


I actually got this pipeline partly from Thomas a few months back. However, I wasn't sure if anyone had suggestions perhaps for a recon-all based command for going from the MNI152 1mm template-based fit to individual subjects. The recon-all/Freesurfer
 inherent striatal parcellations are so well fitted to even my severe AD patients, so I was hoping I could somehow adapt this to the Choi ROIs.



On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl 
 wrote:

Hi Paul

Thomas Yeo (ccd) would be the best person to help you, but he may not be reading email for a while

cheers
Bruce




On Wed, 18 Jun 2014, Paul Beach wrote:


Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.

I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.

NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...

My current pipeline involves two steps:
mri_vol2vol \
--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \
--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest

mri_label2vol \
--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \
--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \
--invertmtx \
--o Choi_17Network_tight_striatum_orig.nii.gz \
--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz

I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain that
would involve.


Thanks for your suggestions.
-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program - MSU Cognitive and Geriatric Neurology Team (CoGeNT)





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-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU Cognitive and Geriatric Neurology Team
 (CoGeNT)








 



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Re: [Freesurfer] freeurfer manual edits

[Harms, Michael]

FWIW: In FS 5.3, -autorecon2-cp and -autorecon2-wm invoke the exact same
set of flags.  (This wasn't the case in earlier versions).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/12/14 10:15 AM, "Bruce Fischl"  wrote:

>Hi Jidan
>
>for your first point, if you make both wm edits and add control points
>you
>can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm.
>
>For the second one, it's hard to diagnose from the single slice. Is there
>white matter through-plane that is not included in the white surface or
>the
>wm.mgz?
>
>cheers
>Bruce
>
>On Thu, 12 Jun 2014, Jidan Zhong wrote:
>
>> Dear FreeSurfer Experts,
>>
>> I have two questions about freesurfer troubleshoot.
>>
>> My subjects are people with multiple sclerosis, so for most of them I
>>need
>> to add control points as well as edit white matter due to lesions. As
>>far as
>> I know, I should add control points and do recon-all -autorecon2-cp
>> -autorecon3  to my subject and then edit white matter, do recon-all
>> -autorecon2-wm -autorecon3.
>>
>> My question is, it seems there are some repeated steps for those two
>>recon
>> steps, and it takes so long to run them. Is there anyway that I can save
>> some process steps and leave it to the last recon? To be specific, can
>>I do
>> recon-all -autorecon2-cp only after I added control points, then do
>> recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is
>> reasonable as after -autorecon2-cp the new white matter surface is
>>already
>> generated and can help to detect wm failure. But I am not sure whether
>>this
>> makes sense to you guys.
>>
>> Another question is, some of my subjects they have degenerated white
>>matter
>> and grey matter, so some parts get so dark that freesurfer would not
>>include
>> it even in the pial surface. I attached one figure for your referece. If
>> there is no white matter detected in that unlabled part (at the top of
>>the
>> figure), what should I do? should I leave it or just add some white
>>matter
>> and control points myself to get a better segmentation and surface?
>>[The
>> case I show in the attachment is much better than some other cases,
>>whose
>> brain has some parts so dark that even I can not tell which is grey
>>matter
>> or white matter from my experience..]
>>
>> Thanks!
>>
>>
>> --
>> Regards,
>>
>> Jidan
>>



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[Freesurfer] mris_convert to GIFTI misaligned in freeview

[Harms, Michael]

Hi,
I converted a surface to GIFTI
e.g.,
mris_convert lh.white lh.white.gii


lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
However, they do not align when loaded simultaneously in 'freeview'.


Of possible relevance: When I loaded lh.white.gii into 'freeview', I got the following message in the terminal:
"Did not find any volume geometry information in the surface"


Is this possibly a bug of some sort in the display of GIFTI surfaces within 'freeview'?


This was all done with FS 5.3.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

[Harms, Michael]

Yes, the S/I/A/P labels are all correct.  (Can never tell with R/L).
So, FSLview is reading the orientation info correctly.  Orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data.  You may not like the manner in which FSLview displays the data, but it
 is respecting the orientation info.


cheers,
-MH






-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 3:20 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL




Please, see the snapshot attached. A/P/S/I/L/R labels seem correct. What do you think
 about?


Thanks,


Stefano







Messaggio originale
Da: mha...@wustl.edu
Data: 29-apr-2014 21.13
A: "std...@virgilio.it"<std...@virgilio.it>, "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>,
 "Harms, Michael"<mha...@wustl.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL








Yes, they need to be the same dimensions to overlay in FSLview.
Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig.






-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL





I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no.


fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)
data_type      FLOAT32
dim1           212
dim2           320
dim3           320
dim4           1
datatype       16
pixdim1        0.80
pixdim2        0.80
pixdim3        0.80
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+




fslinfo Right_Thalamus.nii.gz 
data_type      INT32
dim1           256
dim2           256
dim3           256
dim4           1
datatype       8
pixdim1        1.00
pixdim2        1.00
pixdim3        1.00
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+


fslinfo dtifit_FA.nii.gz 
data_type      FLOAT32
dim1           128
dim2           128
dim3           60
dim4           1
datatype       16
pixdim1        1.75
pixdim2        1.75
pixdim3        2.01
pixdim4        1.00
cal_max        1.
cal_min        0.
file_type      NIFTI-1+








Specifically I have 


1. Registered FreeSurfer conformed structural space to diffusion space
net della T1 e rinominarla come struct_brain


struct<->freesufer
tkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 


fa<-->freesurfer
flirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat 
convert_xfm -omat struct2fa.mat -inverse fa2struct.mat 


convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat 
convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 




2. Creating a label file from FreeSurfer


mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz


mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrict
mri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/label
produce
rh.frontal.label
rh.occipital.label
rh.parietal.label
rh.temporal.label




cd $SUBJECTS_DIR/surf
mris_convert rh.white rh.white.gii
mris_convert lh.white lh.white.gii
echo $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SU

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

[Harms, Michael]

Yes, they need to be the same dimensions to overlay in FSLview.
Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig.






-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL





I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no.


fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)
data_type      FLOAT32
dim1           212
dim2           320
dim3           320
dim4           1
datatype       16
pixdim1        0.80
pixdim2        0.80
pixdim3        0.80
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+




fslinfo Right_Thalamus.nii.gz 
data_type      INT32
dim1           256
dim2           256
dim3           256
dim4           1
datatype       8
pixdim1        1.00
pixdim2        1.00
pixdim3        1.00
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+


fslinfo dtifit_FA.nii.gz 
data_type      FLOAT32
dim1           128
dim2           128
dim3           60
dim4           1
datatype       16
pixdim1        1.75
pixdim2        1.75
pixdim3        2.01
pixdim4        1.00
cal_max        1.
cal_min        0.
file_type      NIFTI-1+








Specifically I have 


1. Registered FreeSurfer conformed structural space to diffusion space
net della T1 e rinominarla come struct_brain


struct<->freesufer
tkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 


fa<-->freesurfer
flirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat 
convert_xfm -omat struct2fa.mat -inverse fa2struct.mat 


convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat 
convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 




2. Creating a label file from FreeSurfer


mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz


mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrict
mri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/label
produce
rh.frontal.label
rh.occipital.label
rh.parietal.label
rh.temporal.label




cd $SUBJECTS_DIR/surf
mris_convert rh.white rh.white.gii
mris_convert lh.white lh.white.gii
echo $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.frontal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.occipital.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.parietal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.temporal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.Right_Thalamus.gii -l listOfAreas_right.txt


echo $SUBJECTS_DIR/label/lh.frontal.label $SUBJECTS_DIR/label/lh.occipital.label $SUBJECTS_DIR/label/lh.parietal.label $SUBJECTS_DIR/label/lh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.frontal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.occipital.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.parietal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.temporal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.Right_Thalamus.gii -l listOfAreas_right.txt



Messaggio originale
Da: mha...@wustl.edu
Data: 29-apr-2014 20.56
A: "std...@virgilio.it"<std...@virgilio.it>, "Harms, Michael"<mha...@wustl.edu>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL






You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy.
It is very unlikely that FSLview is ignoring the orientation information.


cheers,
-MH




-- 
Michael Harm

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

[Harms, Michael]

-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL





I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no.


fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)
data_type      FLOAT32
dim1           212
dim2           320
dim3           320
dim4           1
datatype       16
pixdim1        0.80
pixdim2        0.80
pixdim3        0.80
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+




fslinfo Right_Thalamus.nii.gz 
data_type      INT32
dim1           256
dim2           256
dim3           256
dim4           1
datatype       8
pixdim1        1.00
pixdim2        1.00
pixdim3        1.00
pixdim4        0.011000
cal_max        0.
cal_min        0.
file_type      NIFTI-1+


fslinfo dtifit_FA.nii.gz 
data_type      FLOAT32
dim1           128
dim2           128
dim3           60
dim4           1
datatype       16
pixdim1        1.75
pixdim2        1.75
pixdim3        2.01
pixdim4        1.00
cal_max        1.
cal_min        0.
file_type      NIFTI-1+








Specifically I have 


1. Registered FreeSurfer conformed structural space to diffusion space
net della T1 e rinominarla come struct_brain


struct<->freesufer
tkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 


fa<-->freesurfer
flirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat 
convert_xfm -omat struct2fa.mat -inverse fa2struct.mat 


convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat 
convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat 
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 




2. Creating a label file from FreeSurfer


mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz


mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrict
mri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/label
produce
rh.frontal.label
rh.occipital.label
rh.parietal.label
rh.temporal.label




cd $SUBJECTS_DIR/surf
mris_convert rh.white rh.white.gii
mris_convert lh.white lh.white.gii
echo $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.frontal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.occipital.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.parietal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.temporal.gii -l listOfAreas_right.txt
label2surf -s rh.white.gii -o rh.Right_Thalamus.gii -l listOfAreas_right.txt


echo $SUBJECTS_DIR/label/lh.frontal.label $SUBJECTS_DIR/label/lh.occipital.label $SUBJECTS_DIR/label/lh.parietal.label $SUBJECTS_DIR/label/lh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.frontal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.occipital.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.parietal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.temporal.gii -l listOfAreas_right.txt
label2surf -s lh.white.gii -o lh.Right_Thalamus.gii -l listOfAreas_right.txt



Messaggio originale
Da: mha...@wustl.edu
Data: 29-apr-2014 20.56
A: "std...@virgilio.it"<std...@virgilio.it>, "Harms, Michael"<mha...@wustl.edu>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL






You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy.
It is very unlikely that FSLview is ignoring the orientation information.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University Schoo

Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

[Harms, Michael]

You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy.
It is very unlikely that FSLview is ignoring the orientation information.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 1:52 PM
To: "Harms, Michael" <mha...@wustl.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL






Hi Michael,


please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1). 


Thanks,




Stefano









Messaggio originale
Da: mha...@wustl.edu
Data: 29-apr-2014 20.32
A: "std...@virgilio.it"<std...@virgilio.it>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL





Is the brain merely shown "sideways" in FSLview?  What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have
 an RAS/LAS orientation.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 29, 2014 1:19 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL




Hi Bruce,


in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results.


Thanks,




Stefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 29-apr-2014 17.52
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re:  thalami mask (nii.gz) to import in FSL


How do you know the orientation is wrong? Is it right in tkmedit?

On 04/29/2014 10:23 AM, std...@virgilio.it wrote:
> My apologies, how can I visualize mri_binarize output? I tried in 
> fslview but orientation is wrong. Different orientation is a file's 
> feature or swapdim is request?
>
> Thanks,
>
>
> Stefano
>
>
> Messaggio originale
> Da: fis...@nmr.mgh.harvard.edu
> Data: 29-apr-2014 16.01
> A: <std...@virgilio.it>, "Freesurfer support

> list"<freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL
>
> Hi Stefano
>
> you can use either mri_binarize --match or mri_extract_label with labels
> 10 and 49 (which I got from FreeSurferColorLUT.txt)
>
> cheers
> Bruce
> On Tue, 29 Apr 2014,
> std...@virgilio.it wrote:
>
> > Hi list,
> > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it 
> as seed
> > mask in probtrackx.
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you

> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.

Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

[Harms, Michael]

Is the brain merely shown "sideways" in FSLview?  What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have
 an RAS/LAS orientation.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: "std...@virgilio.it" 
Reply-To: "std...@virgilio.it" , Freesurfer support list 
Date: Tuesday, April 29, 2014 1:19 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL




Hi Bruce,


in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results.


Thanks,




Stefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 29-apr-2014 17.52
A: 
Ogg: Re: [Freesurfer] R: Re:  thalami mask (nii.gz) to import in FSL


How do you know the orientation is wrong? Is it right in tkmedit?

On 04/29/2014 10:23 AM, std...@virgilio.it wrote:
> My apologies, how can I visualize mri_binarize output? I tried in 
> fslview but orientation is wrong. Different orientation is a file's 
> feature or swapdim is request?
>
> Thanks,
>
>
> Stefano
>
>
> Messaggio originale
> Da: fis...@nmr.mgh.harvard.edu
> Data: 29-apr-2014 16.01
> A: , "Freesurfer support

> list"
> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL
>
> Hi Stefano
>
> you can use either mri_binarize --match or mri_extract_label with labels
> 10 and 49 (which I got from FreeSurferColorLUT.txt)
>
> cheers
> Bruce
> On Tue, 29 Apr 2014,
> std...@virgilio.it wrote:
>
> > Hi list,
> > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it 
> as seed
> > mask in probtrackx.
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you

> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer








 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] how to capture blurred GM/WM junction?

[Harms, Michael]

Hi Doug,
Is 'pctsurfcon' intended to supersede 'mri_cnr'?  If not, what are the
intended situations in which one would be used over the other?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 3/24/14 5:21 PM, "Douglas N Greve"  wrote:

>
>you might want to look at the pctsurfcon script to see if that gets you
>where you want to be
>
>On 03/24/2014 06:18 PM, Bruce Fischl wrote:
>> it really depends on the size of the abnormality. I would guess 2 is
>> too big, and you want something more like 1, and sampling not averaging
>> On Mon, 24 Mar 2014, Markus Gschwind wrote:
>>
>>> Hi Bruce!
>>> Ok I see, great! Tank you!
>>>
>>> So to double check, this will be something like :
>>>
>>> mri_vol2surf \
>>>
>>>
>>>   --mov /mri/nu.mgz \
>>>   --ref /mri/nu.mgz \
>>>
>>>   --surf /surf/lh.white
>>>   --projdist mmdist -2 \ # for inside white
>>>
>>>
>>>   # --projdist mmdist 2 \ # for outside white
>>>   --interp trilinear \
>>>   --hemi lh \
>>>   --out lh.nu_inside_white.mgh
>>>
>>>
>>> I am not sure which one to use from those, as I want to compare stable
>>> values but distant from white.
>>>
>>>
>>>--projfrac-avg min max del : average along normal
>>>--projdist mmdist : distance projection along normal
>>>--projdist-avg min max del : average along normal
>>>
>>> What would you recommend?
>>> Thank you again!
>>> Markus
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2014-03-24 21:29 GMT+01:00 Bruce Fischl :
>>>   Hi Markus
>>>
>>>   I wouldn't use brainmask as it has been normalized too
>>>   aggressivley. Maybe the nu.mgz. Look at the difference between
>>>   values just outside of it and just inside of it
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>>>
>>> Dear Bruce,
>>> Thanks for the rapid answer!
>>>
>>> Do you mean that I take the voxel values of
>>> brainmask.mgz at the place where
>>> the ?h.white surface passes, right?
>>>
>>> I thought that the ?l.white surface marks the limit
>>> between GM and WM as a
>>> result of a binary decision.
>>> I would be interested in the local certainty of this
>>> decision. I thought
>>> this is represented by the slope between the values
>>> around 70 and those
>>> >100.
>>>
>>> Thanks again,
>>> Markus
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2014-03-24 19:26 GMT+01:00 Bruce Fischl
>>> :
>>>   Hi Markus
>>>
>>>   I would think that looking at the gray/white
>>> contrast across the
>>>   ?h.white surface would be more informative
>>>
>>>   cheers
>>>   Bruce
>>>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>>>
>>> Dear all,
>>> I would like to capture regions where
>>> the gray
>>> matter/ white matter junction is blurred
>>> in order to
>>> detect possible focal
>>> cortical dysplasias.
>>>
>>> As I understood the WM/GM segmentation
>>> is done by
>>> the script mri_segment.
>>>
>>> Would it be possible detect those
>>> regions where the
>>> gradient between GM and WM regions is
>>> low?
>>>
>>> I imagined that running mri_segment
>>> several times,
>>> with each time a different lower GM
>>> threshold and
>>> higher WM threshold, and
>>> then calculating the diference between
>>> the results,
>>> might give such information.
>>>
>>> I am very much interested in what you
>>> think about
>>> this approach and how to do it
>>> practically.
>>>
>>> For info here are the optional flags of
>>> mri_segment:
>>>
>>> -slope 
>>>
>>> set the curvature slope (both n and p)
>>>
>>> -pslope 
>>>
>>> set the curvature pslope (default=1.0)
>>>
>>> -nslope 
>>>
>>> set the curvature nslope (default=1.0)
>>>
>>> -debug_voxel 
>>>
>>> set voxel for debugging
>>>
>>> -auto
>>>
>>>

Re: [Freesurfer] Calculating Total White Matter

[Harms, Michael]

Hi Elizabeth,
The measure called "CorticalWhiteMatterVol" *is* the total cerebral white
matter.
See this page:
http://freesurfer.net/fswiki/MorphometryStats

The values for the "{lh,rh}CorticalWhiteMatterVol"measures in aseg.stats
used to be the same as that returned by the 'mris_wm_volume' function,
although that changed as of FS 5.2.  (Doug: Why is the output of
'mris_wm_volume' no longer in sync with the output from 'mri_segstats'?
What differs between the two calculations?)

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 3/21/14 1:49 PM, "Adeyemi, Elizabeth (NIH/NIMH) [C]"
 wrote:

>Thank you for your response. But just to clarify a bit further, in the
>asegstats2table there are values given for TotalGrayVol. I am assuming
>this includes both subcortical and cortical measures for GM along with
>cerebellar values, etc. Likewise, I am looking for TotalWhiteVol or a way
>of calculating both cortical and subcortical measures of White Matter
>along with deep tissue values such internal capsules, etc. Your response
>gives me CorticalWhiteMatterVol, as shown in the output. However, I am
>looking for Total Cerebral White Matter. Specifically, I want cortical
>white matter and the volume of deeper cerebral white matter structures
>like internal capsule etc. Which label is ascribed to these deeper
>volumes?
>>
>> Elizabeth Adeyemi
>> On Mar 19, 2014, at 6:27 PM, Douglas N Greve wrote:
>>
>>
>> If you want total cerebral WM, then use the values in aseg.stats
>>
>> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left
>> hemisphere cortical white matter volume, 182991.109375, mm^3
>> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right
>> hemisphere cortical white matter volume, 196871.406250, mm^3
>> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical
>> white matter volume, 379862.515625, mm^3
>>
>>
>> On 03/19/2014 05:48 PM, Adeyemi, Elizabeth (NIH/NIMH) [C] wrote:
>> Hello,
>>
>> I need assistance calculating Total White Matter. Can I simply add
>>Cortical White Matter + Unsegmented White Matter (given in the aseg
>>wmparc output)?
>>
>> Thanks
>>
>> Elizabeth Adeyemi
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>>
>>
>>
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>
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Re: [Freesurfer] Anonymizing Siemens DICOM files

[Harms, Michael]

Hi Caspar,
I can't address your question regarding a specific tool, but wanted to mention a note of caution.
You need to make sure that you scrub any identifying info from Siemen's custom DICOM fields (not just the obvious public DICOM fields).
The challenge of doing that is why the safest thing is to not enter any identifying info at the scanner to begin with.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: "Caspar M. Schwiedrzik" 
Reply-To: Freesurfer support list 
Date: Thursday, March 20, 2014 4:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Cc: Julia Sliwa 
Subject: [Freesurfer] Anonymizing Siemens DICOM files






Hi Freesurfer Experts, 
we are looking for a good way to remove subject names and dates of birth from Siemens DICOM headers. Is there something implemented in Freesurfer?


Matlab's Image Processing Toolbox has a function to anonymize DICOM files (http://www.mathworks.com/help/images/ref/dicomanon.html), but we later run
 into trouble with unpacksdcmdir when we use that. 


Thanks, Caspar







 



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Re: [Freesurfer] expert options command

[Harms, Michael]

You must have already run this subject once with an expert-options file?
Once you've already run recon-all once on a subject with an expert-options file, you don't include it again in future invocations of recon-all.  The expert options that you've previously used will automatically get used again.  You would only need to use
 the -xopts-overwrite option if for some reason you wanted to CHANGE the expert-options you had previously applied.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Michael Green 
Reply-To: Freesurfer support list 
Date: Wednesday, March 19, 2014 11:30 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] expert options command




I've been calling up an expert options file which contains the text "mri_normalize -gentle" but I'm having trouble executing it with this command:


"recon-all -s 002 -expert 002/scripts/expert.opts"

It results in the following error:

ERROR: there is a pre-existing expert options file and
you have specified an expert options file on the command-line.
If you want to use the file specified on the command-line,
you must run with -xopts-overwrite, or you may edit the 
existing file /mridata/workingdata/INS/subjects/002/scripts/expert.opts (and not use the -expert option).

The help message is a little confusing (and not use the -expert option)
but executing 

"recon-all -s 002 -xopts-overwrite 002/scripts/expert.opts" 

gives me the following error:

ERROR: Flag 002/scripts/expert.opts unrecognized.

Any ideas or help on this one?


-- 


Michael Green
Senior Research Officer
Lecturer, UNSW




Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
T +61 2 9399 1086 

neura.edu.au








 



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[Freesurfer] wm.mgz and lh.orig.nofix not matching

[Harms, Michael]

Hi guys,
I was wondering if someone could take a look at a subject that I just uploaded (L217_100908.zip).
An RA was editing wm.mgz to attempt to fix a topology problem in the LH visual cortex.  The edited wm.mgz that she created looks fine to me, but after re-running FS, the surfaces still aren't accurate.  So, I ran 'defect-seg', which still showed a defect
 in that area.  What I then noticed is that lh.orig.nofix doesn't seem to completely respect the borders of wm.mgz.


e.g.,  see volume indexes
141 135 50
141 136 50
140 136 50
140 137 50
139 135 48
139 136 48
138 136 48
138 137 48


For each volume index, wm.mgz has value 1 (indicating that it was edited to "off"), but lh.orig.nofix does not seem to be respecting that setting when the initial white surface is constructed.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



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Re: [Freesurfer] Rotation involved in recon-all

[Harms, Michael]

orig.mgz is not converted to Talairach.  The computed Talairach xfm is
used internally by some stages of recon-all, but none of the volumes are
ever converted to Talairach/MNI space.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/6/14 8:50 AM, "Ed Gronenschild"
 wrote:

>Hi Harm,
>
>Thanks for the trick. Will this, however, give not rise to conversion to
>Talairach
>coordinates?
>
>Cheers,
>Ed
>
>
>On 6 Feb 2014, at 15:38, Harms, Michael wrote:
>
>>
>> Hi Ed,
>> If you want to avoid the rotation (e.g., to avoid an interpolation at
>>the
>> conform step) then you need to manually alter the input so as to remove
>> the off-diagonal elements.  That is in fact what we do as part of our
>> DICOM2NIFTI conversion in the HCP.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.   Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 2/6/14 7:43 AM, "Ed Gronenschild"
>>  wrote:
>>
>>> Hi Bruce,
>>>
>>> Yes, I do understand that is coronal, but there is an actual rotation
>>> apart from an orientation to coronal.
>>> You can read it from the off-diagonal matrix elements.
>>>
>>> Cheers,
>>> Ed
>>>
>>> On 6 Feb 2014, at 14:36, Bruce Fischl wrote:
>>>
>>>> yes, we reorient it to be coronal as part of the "conform" process
>>>>
>>>> cheers
>>>> Bruce
>>>> On Thu, 6
>>>> Feb 2014, Ed Gronenschild wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
>>>>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
>>>>> orig.mgz., see excerpt of output of mri_info below
>>>>>
>>>>> rawavg.mgz:
>>>>>
>>>>>  xform info: x_r =   0.0081, y_r =  -0.0913, z_r =   0.9958, c_r =
>>>>> 0.0813
>>>>>: x_a =  -0., y_a =  -0.0066, z_a =   0.0076, c_a =
>>>>> 14.8386
>>>>>: x_s =   0.0059, y_s =  -0.9958, z_s =  -0.0913, c_s =
>>>>> 13.1335
>>>>>
>>>>> orig.mgz:
>>>>>
>>>>>  xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =
>>>>> 0.0813
>>>>>: x_a =   0., y_a =  -0., z_a =   1., c_a =
>>>>> 14.8386
>>>>>: x_s =   0., y_s =  -1., z_s =   0., c_s =
>>>>> 13.1335
>>>>>
>>>>>
>>>>> Is that the default way of processing the data?
>>>>>
>>>>> Cheers,
>>>>> Ed
>>>>>
>>>>>
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender
>>>>and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>
>>>
>>> ___
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>>
>>
>> 
>> The materials in this message are private and may contain Protected
>>Healthcare Information or other information of a sensitive nature. If
>>you are not the intended recipient, be advised that any unauthorized
>>use, disclosure, copying or the taking of any action in reliance on the
>>contents of this information is strictly prohibited. If you have
>>received this email in error, please immediately notify the sender via
>>telephone or return mail.
>



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Re: [Freesurfer] Rotation involved in recon-all

[Harms, Michael]

Hi Ed,
If you want to avoid the rotation (e.g., to avoid an interpolation at the
conform step) then you need to manually alter the input so as to remove
the off-diagonal elements.  That is in fact what we do as part of our
DICOM2NIFTI conversion in the HCP.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/6/14 7:43 AM, "Ed Gronenschild"
 wrote:

>Hi Bruce,
>
>Yes, I do understand that is coronal, but there is an actual rotation
>apart from an orientation to coronal.
>You can read it from the off-diagonal matrix elements.
>
>Cheers,
>Ed
>
>On 6 Feb 2014, at 14:36, Bruce Fischl wrote:
>
>> yes, we reorient it to be coronal as part of the "conform" process
>>
>> cheers
>> Bruce
>> On Thu, 6
>> Feb 2014, Ed Gronenschild wrote:
>>
>>> Hi,
>>>
>>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
>>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
>>> orig.mgz., see excerpt of output of mri_info below
>>>
>>> rawavg.mgz:
>>>
>>>   xform info: x_r =   0.0081, y_r =  -0.0913, z_r =   0.9958, c_r =
>>> 0.0813
>>> : x_a =  -0., y_a =  -0.0066, z_a =   0.0076, c_a =
>>>14.8386
>>> : x_s =   0.0059, y_s =  -0.9958, z_s =  -0.0913, c_s =
>>>13.1335
>>>
>>> orig.mgz:
>>>
>>>   xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =
>>> 0.0813
>>> : x_a =   0., y_a =  -0., z_a =   1., c_a =
>>>14.8386
>>> : x_s =   0., y_s =  -1., z_s =   0., c_s =
>>>13.1335
>>>
>>>
>>> Is that the default way of processing the data?
>>>
>>> Cheers,
>>> Ed
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>>
>
>
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Re: [Freesurfer] Autorecon2 Pipeline Problem

[Harms, Michael]

Hi Chad,
Why do you say the Segmentation step overwrites your WM edits?  We've just run WM edits under FS 5.3 very recently and it worked fine.  Also, a glance at the recon-all script indicates that the Segmentation step is testing for the presence of existing
 edits.


cheers,
-MH



-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: , Chad P 
Date: Tuesday, February 4, 2014 10:27 AM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Autorecon2 Pipeline Problem








Good morning,
 
I am new to the e-mail list and would like to request help with a problem that has arisen when running recon-all.  As such, I apologize if this question has been posed previously.  We are running Freesurfer version 5.3.0 on Red Hat Enterprise
 Linux Release 6.3 using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 stable release of Freesurfer. 

 
Following white matter edits, the invocation “recon-all –autorecon2-wm –s ” begins at the Normalization 2 step, rather than the Fill step as stated in the processing stages pipeline.  This is problematic as the following segmentation
 step overwrites the edited wm.mgz file with new automated information.  Review of the output also indicates that the wm.mgz is being regressed back to the pre-edited state.  A check of the recon-all lib file revealed the following.
 
recon-all lib file source code from version 5.3.0 (lines 5465 through 5482):
 
    case "-autorecon2-cp":
    case "-autorecon2-noaseg":
    case "-autorecon2-wm":
  set DoNormalization2 = 1;
  set DoSegmentation   = 1;
  set DoFill   = 1;
  set DoTessellate = 1;
  set DoSmooth1    = 1;
  set DoInflate1   = 1;
  set DoQSphere    = 1;
  set DoFix    = 1;
  set DoMaskBFS    = 1;
  set DoWhiteSurfs = 1;
  set DoSmooth2    = 1;
  set DoInflate2   = 1;
  set DoSegStats   = 1;
  set DoCurvStats  = 1;
  breaksw
 
Where it appears that –cp, –noaseg, and –wm are all aliases of the same command.  This differs significantly from the previous release we used in the lab of 5.1.0.
 
recon-all lib file source code from version 5.1.0 (lines 4806 through 4819):
 
    case "-autorecon2-wm":
  set DoFill   = 1;
  set DoTessellate = 1;
  set DoSmooth1    = 1;
  set DoInflate1   = 1;
  set DoQSphere    = 1;
  set DoFix    = 1;
  set DoMaskBFS    = 1;
  set DoWhiteSurfs = 1;
  set DoSmooth2    = 1;
  set DoInflate2   = 1;
  set DoSegStats   = 1;
  set DoCurvStats  = 1;
  breaksw
 
I assume that I can modify my pipeline with some –no commands to keep the DoNormalization2 and DoSegmentation steps from running but I was wondering if there was a reason for the change between versions which would argue against starting
 at the fill stage following white matter edits.  I can provide any additional information if needed to help solve this problem and any information that can be provided regarding this would be most helpful.  Thanks.
 
 
Chad P. Johnson, Ph.D.
Postdoctoral Fellow
University of Texas Health Science Center






 



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[Freesurfer] Editing-related Wiki pages

[Harms, Michael]

Hi,
I see that the links off of 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
now provide instructions for editing via Freeview rather than Tkmedit.


I found the older instructions for editing via Tkmedit still available by appending "_tktools" rather than "_freeview".
e.g.,
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools


For those who are familiar with editing via Tkmedit, I assume that it is ok to continue making edits via Tkmedit?


Also, wanted to mention that the links off this page are currently broken:
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
and suggest that during a transition period that you maybe include explicit links to the _tktools variants of the editing instructions as well, so that users can easily find the instructions for the older editing approaches that they may be most familiar
 with.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
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Re: [Freesurfer] Multiple Frames

[Harms, Michael]

BTW: If you download the structural preprocessed data, the HCP data
already includes aparc+aseg.nii.gz in both "native" space and transformed
to MNI152 space.  If you want the data values contained in the native
space aseg.stats file of FreeSurfer, you can quickly get that as part of
the spreadsheet of data available for each subject at
db.humanconnectome.org

cheers,
-MH


--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/22/14 11:47 AM, "Bruce Fischl"  wrote:

>that's what I wondered. AFI = "Actual Flip angle Imaging" usually
>On Wed, 22
>Jan 2014, Glasser, Matthew wrote:
>
>> AFI is a bias transmit scan, not an MPRAGE.  Look for T1w.
>>
>> On 1/22/14 11:44 AM, "Bruce Fischl"  wrote:
>>
>>> Hi Al,
>>>
>>> can you run mri_info on  100307_3T_AFI.nii? Is that an AFI scan? I'm
>>>not
>>> familiar with their naming convention. I'll cc Matt Glasser who can
>>> probably help.
>>>
>>> cheers
>>> Bruce
>>>  On Wed, 22 Jan 2014, Alfred Ochs wrote:
>>>
 Hello folks,

 I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI
 structural T1
 MRI from the Human Connectome Project, in particular
 100307_3T_AFI.nii.  Unless I am mistaken, their preprocessed data
 doesn't
 include aseg data, at least identified in a manner I am familiar
 with.  Nevertheless,  recon-all -s 100307_cs -all reports:

 ERROR: input(s) cannot have multiple frames!
 /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2
 frames.

 How do I work around this?

 Thanks,  Al

 Alfred L. Ochs, Ph.D.
 Virginia Institute for Neuropsychiatry
 Richmond, Virginia


>>>
>>>
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>>>it
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>>> addressed. If you believe this e-mail was sent to you in error and the
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>>
>>
>> 
>> The materials in this message are private and may contain Protected
>>Healthcare Information or other information of a sensitive nature. If
>>you are not the intended recipient, be advised that any unauthorized
>>use, disclosure, copying or the taking of any action in reliance on the
>>contents of this information is strictly prohibited. If you have
>>received this email in error, please immediately notify the sender via
>>telephone or return mail.
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Re: [Freesurfer] brain orientation in qdecDouglas N Greve

[Harms, Michael]

The surface initially loads upside down, and if you load the annotations
the ensuing parcellations are mapped to an upside down surface
appropriately, but the label reported in the 'Tksurfer Tools' window
appears to be based on a right-side-up brain.
For example, if I position the cursor over the brown patch that is the
"caudal middle frontal" region, the "Mouse" position says
"middletemporal".  If I then click at that location, the "Cursor" label
changes to "middletemporal" as well, but the funny thing is that region
that shows up outlined in yellow, and the position of the asterisk that
gets placed on the surface is indeed the middle temporal region (i.e., at
the top of the Tksurfer window since the brain is upside-down).

Does that make sense?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/13/14 12:51 PM, "Bruce Fischl"  wrote:

>Hi Mike
>
>what kind of mismatch do you mean?
>Bruce
>On Mon, 13 Jan 2014, Harms, Michael
>wrote:
>
>>
>> To add to this thread, I have this same problem (upside-down display in
>> tksurfer, with mismatch with the reported annotation labels in the Tools
>> window) when using a CentOS 6.4 system, using both FS 5.1 and FS 5.3,
>>but
>> not when using a CentOS 5.5 system.
>>
>> If there is an easy fix for this (environment or system variable of some
>> sort?) that would be very helpful to know.
>>
>> thanks,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: Doug Greve 
>> Date: Sunday, January 12, 2014 11:34 AM
>> To: "Schweren, LJS (med)" , free surfer
>> 
>> Subject: Re: [Freesurfer] brain orientation in qdecDouglas N Greve
>>
>>
>> Sounds like it is some problem with the display libraries. I think
>>someone
>> else was having the same problem recently (ie, hemisphere displayed
>>upside
>> down in tksurfer). Does anyone remember? Zeke?
>> doug
>>
>>
>>
>>
>>
>> On 1/12/14 5:03 AM, Schweren, LJS (med) wrote:
>>
>> No, in Freeview I encountered no such problems. Also in tkmedit the
>>brains a
>> ppear in normal orientation.
>> Also, the scale bars and titles are displayed upside down in tksurfer.
>>
>> Best, Lizanne
>>
>>
>>
>> Does the same thing happen in freeview?
>>
>> On 01/06/2014 04:45 AM, L. Schweren wrote:
>> >
>> > Dear experts,
>> >
>> > I ran recon-all with qcache. When loading the right hemisphere of
>> > fsaverage (or any other surface reconstruction) into tksurfer (for
>> > example command: tksurfer fsaverage rh white), the left hemisphere
>> > surface is displayed, and it is upside down. When I import
>>annotations
>> > they load in the same orientation as the surface. However, the
>> > coordinates and the labels, displayed in the Tksurfer Tools window,
>> > are not. For example, when I move the cursor to the temporal lobe,
>>the
>> > label says it¹s postcentral. I do not mind manually turning the
>> > surfaces in tksurfer, but I do need to be sure I am looking at the
>> > correct hemispheres, coordinates and labels.
>> >
>> > I hope you can help me solve this. Thank you in advance.
>> >
>> > Best wishes,
>> >
>> > Lizanne
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.



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Re: [Freesurfer] brain orientation in qdecDouglas N Greve

[Harms, Michael]

To add to this thread, I have this same problem (upside-down display in tksurfer, with mismatch with the reported annotation labels in the Tools window) when using a CentOS 6.4 system, using both FS 5.1 and FS 5.3, but not when using a CentOS 5.5 system.


If there is an easy fix for this (environment or system variable of some sort?) that would be very helpful to know.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Doug Greve 
Date: Sunday, January 12, 2014 11:34 AM
To: "Schweren, LJS (med)" , free surfer 
Subject: Re: [Freesurfer] brain orientation in qdecDouglas N Greve





Sounds like it is some problem with the display libraries. I think someone else was having the same problem recently (ie, hemisphere displayed upside down in tksurfer). Does anyone remember? Zeke?
doug





On 1/12/14 5:03 AM, Schweren, LJS (med) wrote:



No, in Freeview I encountered no such problems. Also in tkmedit the brains appear in normal orientation. 
Also, the scale bars and titles are displayed upside down in tksurfer. 

Best, Lizanne



Does the same thing happen in freeview?

On 01/06/2014 04:45 AM, L. Schweren wrote:
>
> Dear experts,
>
> I ran recon-all with qcache. When loading the right hemisphere of 
> fsaverage (or any other surface reconstruction) into tksurfer (for 
> example command: tksurfer fsaverage rh white), the left hemisphere 
> surface is displayed, and it is upside down. When I import annotations 
> they load in the same orientation as the surface. However, the 
> coordinates and the labels, displayed in the Tksurfer Tools window, 
> are not. For example, when I move the cursor to the temporal lobe, the 
> label says it’s postcentral. I do not mind manually turning the 
> surfaces in tksurfer, but I do need to be sure I am looking at the 
> correct hemispheres, coordinates and labels.
>
> I hope you can help me solve this. Thank you in advance.
>
> Best wishes,
>
> Lizanne
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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