date:20161031

Re: [Freesurfer] Two Stage Longitudinal Model

2016-10-31 Thread Timothy Hendrickson

Hi Martin,

Thank you for your reply. I am glad to hear that I am doing that correctly.
I am running into an error when I attempted to run my GLM.

I have looked at my fsgd and qdec files for errors, however I cannot seem
to find anything.

The error is in the attached .txt file named
illCondMatrix_twoStage_years_10_31_16.txt.

Additionally I've included my fsgd file for stage two and my qdec file for
stage one.

Any assistance would be extremely helpful,

-Tim



Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
Normalized matrix condition is 129299
Design matrix --
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.995;
 1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.010   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.050;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000   0.000   0.555   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   1.010   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   1.005   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.010   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.005;
 0.000   0.000   1.000   0.000   0.000   0.000   1.035   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.495   0.000;
 1.000   0.000   0.000   0.000   0.995   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   1.000   0.000   0.000;
 1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.985   0.000   0.000;
 1.000   0.000   0.000   0.000   0.990   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.980;
 0.000   1.000   0.000   0.000   0.000   0.980   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000   0.000   0.990   0.000   0.000;
 1.000   0.000   0.000   0.000   0.990   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.990;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.990;
 1.000   0.000   0.000   0.000   0.985   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.985   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.010   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.985   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.995   0.000;
 1.000   0.000   0.000   0.000   0.995   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   1.450   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.990   0.000;
 0.000   1.000   0.000   0.000   0.000   0.995   0.000   0.000;
 1.000   0.000   0.000   0.000   0.995   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.995   0.000;

ERROR: matrix is ill-conditioned or badly scaled, condno = 129299

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --glmdir 
rh.UMN.gender.group.Years.thickness.fwhm10.twoStage.glmdir --fsgd 
twoStageLongitudinal_BaseUMN_Gender_Group_Years.fsgd dods --y 
rh.testretest.thickness-pc1.stack.fwhm10.mgh --C 
DiffDiagnosis_ControlMore_AcctGender_AcctYearDiff_twoStage_10_25_16.mtx --C 
DiffDiagnosis_ControlMore_AcctGender_YearDiffSlope_twoStage_10_25_16.mtx --C 
DiffGender_MaleMore_AcctGroup_AcctYearDiff_twoStage_10_25_16.mtx --C 
DiffGender_MaleMore_AcctGroup_YearDiffSlope_twoStage_10_25_16.mtx --C 
YearDiff_AcctGender_AcctSite_twoStage_10_25_16.mtx --label 
rh.testretest.fsaverage.cortex.label --surf fsaverage rh 
  2. The FSGD file (if using one)
  3. And the design matrix above



twoStageLongitudinal_BaseUMN_Gender_Group_Years.fsgd
Description: Binary data


twoStage_UMN_Group_Sex_Years.table.dat
Description: Binary data
___
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] Longitudinal analysis

2016-10-31 Thread Jaiashre Sridhar

Hi FreeSurfer Team,

We are doing a longitudinal analysis with three time points which are six 
months apart. The subjects at any time point were scanned on either one of the 
two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our 
analysis. Most of the subjects show decrease in cortical volume over time 
except a few of them, who show a huge increase in volume at their 6th-month 
visit (or at their 12th-month in a couple of cases).
When we tried to look at the reconstructed surfaces of the long brains in 
Freeview, the gray matter and white matter boundaries of the 6th-month were 
bigger overall than the boundaries of the baseline and 12th-month.
Could you share with us your thoughts on what factors (with 
MPRAGE/Scanner/FreeSurfer) might have caused this problem?

Thank you,
Jaiashre.

___
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] Amygdala subfields

2016-10-31 Thread Dorit Kliemann

to clarify: the amygdala subregion atlas is built and will be released early 
2017.

Dorit

On Oct 31, 2016, at 11:46 AM, Dorit Kliemann  wrote:

> Hi Sascha,
> yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
> subfields . Its currently being tested and to be implemented (hopefully) 
> soon. Stay tuned. 
> 
> Dorit
> 
> 
>> From: "sf" 
>> Subject: [Freesurfer] Amygdala subfields
>> Date: 31 October 2016 at 15:13:21 GMT
>> To: "'Freesurfer support list'" 
>> Reply-To: Freesurfer support list 
>> 
>> Hi all, is there any possibility to segment amygdala subfields with 
>> freesurfer? Similar to the hippocampal subfields segmentation?
>> Cheers - Sascha
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 

smime.p7s
Description: S/MIME cryptographic signature
___
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] fsaverage_sym LR-flipchecks

2016-10-31 Thread James Roe

Hi Doug


Thanks for the reply. It's actually just a normal first level fMRI analysis ran 
once on subj1 and once on subj1 after flipping the anatomical and BOLD data for 
subj1. After flipping I ran recon-all on the flipped subject (treating as new 
subject - so for this sub LH == RH)


Top left images = fMRI for subj1? and subj1_flipped - smoothing and 
analysis performed on fsaverage_sym

Top right images = ?fMRI for subj1? and subj1_flipped - smoothing and 
analysis performed on individual surface (with --self)


The images below are the respective analyses resampled onto the surface in 
which the analysis was not performed


I expected the output to be symmetrical (because input is subj1 and 
subj1_flipped).

However, the analysis performed on fsaverage_sym comes out less symmetrcial 
than when performed on --self


I was wondering if you know why this is?



(Resampling each onto the other surface I think shows that it is not a bias 
introduced during recon-all of subj1_flipped because the output is still more 
symmetrical when performed on individual surface and resampled onto 
fsaverage_sym)


thanks!


James


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: 28 October 2016 18:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsaverage_sym LR-flipchecks


Hi James, this looks like a fairly complicated analysis, and I'm not sure I 
understand it all. Are the overlays fMRI or thickness results? How did you 
generate, for example, the top left images?

On 10/26/16 3:15 AM, James Roe wrote:

?

Hi Freesurfer experts



I have an ultimate goal of performing direct LH v RH comparisons using the 
fsaverage_sym template, so these pre-analysis steps are aiming to assess the 
symmetry of the template.



I have performed a first-level fMRI analysis on a subject and am using this to 
compare the output with the exact same analysis performed on the same subject 
with LR-flipped data (anatomical, BOLD runs and B0 maps). I then ran recon-all 
on this flipped subject (treating flipped subject as new subject).

Attached is a screenshot showing the different analysis outputs.



In the top left image, analyses have been performed and smoothed on 
fsaverage_sym (RH shows LH flipped anat and BOLD data). As you can see, 
agreement is generally high, but there are also marked differences, most 
notably in postcentral/precentral regions.

The bottom left shows this output resampled onto the individual surface (for 
comparison purposes for the next analysis).



The top right image shows the output when analyses were performed on the 
individual surfaces of the original and flipped subject. Here, agreement seems 
much higher, also in postcentral/precentral regions (although still not 
symmetrical). The bottom right image shows this output resampled onto 
fsaverage_sym, and agreement remains very high.



So it seems that performing the analysis on fsaverage_sym itself may be 
affecting the expected symmetry of the output. Originally I aimed to perform a 
comparison of the vectors of B-values in order to prove symmetry, although I am 
not sure whether this is a viable option anymore. Do you have any advice as to 
how I could proceed with this?



Finally, it appears that also in the fsaverage_sym template the L/R vertices do 
not correspond to one another. So will it be possible to flip the analysis 
values and template in order to perform LH v RH comparisons at the group level?



System: Linux CentOS 6 x86_64 (64b) stable v5.3.0



Thank you for your time

James





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


___
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] Creating overlay files automatically

2016-10-31 Thread Douglas Greve

Look up the specs for nifti files. The spec is publicly available. If 
you are doing this in matlab, you can use our MRIwrite.m



On 10/31/16 6:01 AM, Eloy Geenjaar wrote:


Dear Douglas,

Thanks for the quick response, I do know that nifti or mgz files are 
used for the overlay, I was trying to figure out how to write such 
files though. In what format do I have to write nifti or mgz files for 
Freeview to be able to load them correctly?


Kind regards,

Eloy Geenjaar


*Van:* freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Douglas Greve 


*Verzonden:* vrijdag 28 oktober 2016 17:19
*Aan:* freesurfer@nmr.mgh.harvard.edu
*Onderwerp:* Re: [Freesurfer] Creating overlay files automatically

We usually create nifti or mgz files to use as overlays both for the 
volume or the surface. Is this what you mean?



On 10/28/16 9:17 AM, Eloy Geenjaar wrote:


Dear Freesurfer Experts,


I am a student at the technical university of Delft and currently 
working on a project to automatically visualize the cortical 
thickness data of children. To automatically visualize the data I 
want to use Freeview, to use Freeview as visualization tool I have to 
write brain specific layout files. To do this automatically I want to 
know what the layout for the overlay files is, so Freeview can read 
them automatically. The data for the layout files should be different 
per brain, I have already acquired the data and I am ready to 
write it to a layout file, but I can't figure out what the standard 
way of writing a layout file is, without having to manually do 
anything. The language in which I want to write the code is Python.



Kind regards,


Eloy Geenjaar



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




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


___
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] Recon-all Exiting without Error

2016-10-31 Thread Douglas Greve


To answer your question, you need to tell recon-all what to do. Eg, -all


On 10/31/16 10:47 AM, Harms, Michael wrote:


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  63110Email: mha...@wustl.edu

From: > on behalf of Natalie 
Busby >
Reply-To: Freesurfer support list >

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



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


___
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] Amygdala subfields

2016-10-31 Thread Dorit Kliemann

Hi Sascha,
yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
subfields . Its currently being tested and to be implemented (hopefully) soon. 
Stay tuned. 

Dorit


> From: "sf" 
> Subject: [Freesurfer] Amygdala subfields
> Date: 31 October 2016 at 15:13:21 GMT
> To: "'Freesurfer support list'" 
> Reply-To: Freesurfer support list 
> 
> Hi all, is there any possibility to segment amygdala subfields with 
> freesurfer? Similar to the hippocampal subfields segmentation?
> Cheers - Sascha
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 


smime.p7s
Description: S/MIME cryptographic signature
___
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] values of 0 in the beta.mgh files

2016-10-31 Thread Douglas Greve


If you use the --no-prune flag, then it will consider all subjects at a 
vertex regardless of whether it is 0 or not. But is this really what you 
want to do?


 >>Thank you so much for the reply. Yes I do se now, that single 
subjects which have certain vertexes with a value of 0 thus excludes 
that vertex for analyses for all subjects. Is there a flag to exclude 
just the >>vertex of the individuals with 0 and keep the vertex for the 
rest of the subjects?
 >>If not I Guess a possibility is the "--no-prune" flag.


On 10/31/16 8:50 AM, l.c.b.nor...@psykologi.uio.no wrote:
> On 2016-10-27 17:26, Douglas N Greve wrote:
>> Yes, if even one subject has a 0 at a vertex, then that vertex will be
>> excluded from analysis
>>
>>
>> On 10/27/2016 10:34 AM, Bruce Fischl wrote:
>>> Hi Linn
>>> can you show us a picture of the medial inflated surface with the 
>>> overlay?
>>> The occipital horn of the ventricle is quite difficult to label and
>>> sometimes erroneously extends into the anterior calcarine. If this 
>>> is tthe
>>> location of your 0s you should correct the aseg and rerun with -make 
>>> all to
>>> get the ?h.cortex.label and the surfaces right
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 27 Oct
>>> 2016, l.c.b.nor...@psykologi.uio.no wrote:
>>>
 Hello Freesurfer Developers,

 I am having an issue with values of 0 in certain areas of the visual
 cortex in my beta.mgh files.


 I am looking at the effect of age on grey/white matter signal 
 intensity
 contrast (grey devided by white times 100) with gender as a 
 regressor. I
 ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were 
 males
 and females respectively and age in months was the variable.

 When I look at the beta.mgh files in Freeview there are identical 
 parts
 of surface which contains 0 even tho there are contrast values in 
 those
 areas in the contrast surface maps. If I understood correctly the 2
 first beta files should be the average contrast for males and 
 females at
 offset? and the 3rd and 4th should be the slope? So at least the first
 two files should not contain 0 other than in the medial wall.

 Any idea what I might be doing wrong?

 Thank you in advance!
 Cheers, Linn
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



>>> ___
>>> 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 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.
>
> Thank you so much for the reply. Yes I do se now, that single subjects 
> which have certain vertexes with a value of 0 thus excludes that 
> vertex for analyses for all subjects. Is there a flag to exclude just 
> the vertex of the individuals with 0 and keep the vertex for the rest 
> of the subjects?
>
> If not I Guess a possibility is the "--no-prune" flag.
>
> Cheers,
>
>

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

Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

2016-10-31 Thread Quinn McLellan

Hey Martin,


Thank you for the reply.

Yes, I ended up recreating the table solely within a text editor and it worked 
so it was some sort of formatting issue.

Thank you for your time.



Quinn


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: October 29, 2016 3:38:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

Quinn,

Could be that the table has any strange character in it (e.g. strange white 
space etc. )

Try to create a table in a simple text editor by typing the header line and the 
first 1 or two rows (space separated). If it can read that, then it is probably 
the format of your table.

Best, Martin


On Oct 21, 2016, at 9:24 PM, Quinn McLellan 
mailto:quinn.mclel...@ucalgary.ca>> wrote:

Dear Freesurfer team,

I am trying to perform qdec longitudinal analysis.
I have ran produced the template and long files, as well as the longitudinal 
table.

I am currently trying to perform the long_mis_slopes command however I keep 
getting:
ERROR: qdec table /qdec/long.qdec.respsex.table.dat not found or empty?

I am using
Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
Platform: OS X El Capitan

The table does exist, however, I keep getting the same error. The table has the 
columns that are specified as being necessary (fsid, fsid-base, and an age 
column - "days" in my case). Currently it also has a response and sex column. I 
have changed the age column to "years", changed the location in/out of my 
subjects folder into a 'qdec' folder within /subjects. I removed the fsid 
column and received an error output of
ERROR: qdec table missing correct column headers?
   Make sure first column is labeled 'fsid' for the time point and
   second column is 'fsid-base' to specify the subject tempate (base), e.g.:

 fsidfsid-base   age
 me1 me  22.3
 me2 me  23.2
 you1you 21.6
 you2you 22.5

suggesting that it can see the .dat table. Additionally, from the terminal I 
can open the table in microsoft excel, pico etc.
However, it fails when it tries to parse the table.

I have attached a log of the varying attempts I have made to use the 
long_mris_slopes command.
I have also attached what is essentially the .dat table I have been trying to 
use for your viewing as well.
I've searched the list and can't seem to find discussion of this error with 
regards to the long_mis_slopes command.
Am I missing something?
Does anyone have any thoughts on how to trouble shoot this?

Thank you.

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

___
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] Amygdala subfields

2016-10-31 Thread sf

Hi all, is there any possibility to segment amygdala subfields with freesurfer? 
Similar to the hippocampal subfields segmentation?

Cheers - Sascha

___
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] Obtain images extracted from aseg.mgz that have been corrected for partial volume effects

2016-10-31 Thread Andrea Shafer

Hi Bruce,  This would be most helpful. And yes, I think multiple labels for
each voxel that are the coefficients that explain the observed intensity of
that voxel would be a good format. I am thinking that anyone could then
correct for pve of structures taken from the aseg.mgz file in matlab (or
python) by keeping or removing voxels on the border of the structure based
on which tissue class as the highest coefficient. Does this seem reasonable
to you? Is that how the --pv flag for mri_segstats works (i.e., by making
the decision to keep or discard a voxel based on the tissue class with the
highest coefficient)?

Many thanks,
Andrea

Hi Andrea

sorry, I don't think we do, although could add such a thing I guess, although
the format isn't clear to me. I guess you would have to save multiple
labels at each voxel with the mixing coefficient of each one.

cheers
Bruce

On Tue, Oct 25, 2016 at 8:57 PM, Andrea Shafer 
wrote:

> Hello FreeSurfer Developers,
>
> I'm attempting to create partial volume (pve) corrected images for some of
> the subcortical segmentations. I have searched the list and found
> discussions regarding how the volumes for pve corrected data can be
> obtained by default with the asegstats2table command, or when using the
> mri_segstats command with the --pv flag. However, I am wondering if it is
> possible to save the mixed coefficient map of the pve correction process or
> save a aseg.mgz file that has been pve corrected?
>
> Sincerely,
> Andrea
>
___
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] Recon-all Exiting without Error

2016-10-31 Thread 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



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.

[Freesurfer] Recon-all Exiting without Error

2016-10-31 Thread Natalie Busby

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

___
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] Extend pial surface

2016-10-31 Thread Bruce Fischl


Hi Noah

it's impossible to tell from a single slice, but if you are talking about 
the right superior temporal gyrus I would guess that it is an incorrectly 
fixed topological defect. If you upload the subject to our ftp site we will 
take a look


cheers
Bruce


On Mon, 31 Oct 2016, Noah Markowitz wrote:


Hi all, I’m trying to extend the pial surface to include missing GM. Part of
the problem is that the wm.mgz seems to include the WM, but does not extend
the border of the pial surface. I’ve attached links to pictures of the one
of the scans. Any help would be greatly appreciated.
Noah

Without wm.mgz
overlay: http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png
With mg.mgz
overlay: http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png



___
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] [Question for recommended MRI protocols]

2016-10-31 Thread Bruce Fischl


Hi Jeongsik

the bandwidth, geometry and read-out matching ensure that there is no 
differential distortion between the scans, so unless you have a 
compelling reason I wouldn't change any of that.


And you definitely, definitely cannot reduce the voxel size to 2mm iso 
and expect to get anything reasonable.


cheers
Bruce
On Mon, 31 Oct 2016, 김정식 
wrote:




Dear Freesurfer experts,

Regarding the recommended MRI protocol for FreeSurfer,

We have some questions.


I read that using T1 Multiecho MPRAGE and T2-SPACE FLAIR in the Freesurfer
analysis would be helpful to enhance a Freesurfer result.

T2-SPACE FLAIR image must have both same voxel resolution (1x1x1) and
bandwidth(651 Hz/px) equal to T1 image?

Is it possible to change voxel resolution of the T2-SPACE FLAIR to lower one
(eg. 2x2x2), guaranteeing same Freesurfer result?


And one MRI expert recommended that T2-SPACE FLAIR should be acquired in
axial orientation, not in sagittal orientation.

Is it right?

I'm wondering what the difference is between axial and sagittal acquisition
orientation in the aspect of MRI quality and analysis result.


Best regards,

Jeongsik Kim



[@from=gitamen%40hanmail.net&rcpt=freesurfer%40nmr.mgh.harvard.edu&msgid=%3
C20161031103710.AFiqCWu0REKT7xuZN-rV5A%40gitamen.hanmail.net%3E]
___
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] values of 0 in the beta.mgh files

2016-10-31 Thread l . c . b . norbom

On 2016-10-27 17:26, Douglas N Greve wrote:
> Yes, if even one subject has a 0 at a vertex, then that vertex will be
> excluded from analysis
> 
> 
> On 10/27/2016 10:34 AM, Bruce Fischl wrote:
>> Hi Linn
>> can you show us a picture of the medial inflated surface with the 
>> overlay?
>> The occipital horn of the ventricle is quite difficult to label and
>> sometimes erroneously extends into the anterior calcarine. If this is 
>> tthe
>> location of your 0s you should correct the aseg and rerun with -make 
>> all to
>> get the ?h.cortex.label and the surfaces right
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Thu, 27 Oct
>> 2016, l.c.b.nor...@psykologi.uio.no wrote:
>> 
>>> Hello Freesurfer Developers,
>>> 
>>> I am having an issue with values of 0 in certain areas of the visual
>>> cortex in my beta.mgh files.
>>> 
>>> 
>>> I am looking at the effect of age on grey/white matter signal 
>>> intensity
>>> contrast (grey devided by white times 100) with gender as a 
>>> regressor. I
>>> ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were 
>>> males
>>> and females respectively and age in months was the variable.
>>> 
>>> When I look at the beta.mgh files in Freeview there are identical 
>>> parts
>>> of surface which contains 0 even tho there are contrast values in 
>>> those
>>> areas in the contrast surface maps. If I understood correctly the 2
>>> first beta files should be the average contrast for males and females 
>>> at
>>> offset? and the 3rd and 4th should be the slope? So at least the 
>>> first
>>> two files should not contain 0 other than in the medial wall.
>>> 
>>> Any idea what I might be doing wrong?
>>> 
>>> Thank you in advance!
>>> Cheers, Linn
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> 
>> ___
>> 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 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.

Thank you so much for the reply. Yes I do se now, that single subjects 
which have certain vertexes with a value of 0 thus excludes that vertex 
for analyses for all subjects. Is there a flag to exclude just the 
vertex of the individuals with 0 and keep the vertex for the rest of the 
subjects?

If not I Guess a possibility is the "--no-prune" flag.

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

[Freesurfer] recon-all steps question

2016-10-31 Thread miracle ozzoude

Hello Freesurfer,
I have couple of questions. While going through the frequently asked
questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I
came across a question regarding how to integrate a skull stripped from
another problem into freesurfer (using recon-all -autorecon1 -noskullstrip
-s subjid > create a symbolic link from T1.mgz to brainmask.auto.mgz
and another like from brainmask.auto.mgz to brainmask.mgz --> after run
the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s
subjid).

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag?

Second question, where do I insert my already skull stripped data in the
symbolic link?

Last question, the final stages of recon-all doesn't include skull
stripping, how can I be sure my skull stripped data was incorporated into
the freesurfer recon-all process?

Best,
Paul
___
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] Creating overlay files automatically

2016-10-31 Thread Eloy Geenjaar

Dear Douglas,



Thanks for the quick response, I do know that nifti or mgz files are used for 
the overlay, I was trying to figure out how to write such files though. In what 
format do I have to write nifti or mgz files for Freeview to be able to load 
them correctly?



Kind regards,



Eloy Geenjaar



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Douglas Greve 

Verzonden: vrijdag 28 oktober 2016 17:19
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Creating overlay files automatically


We usually create nifti or mgz files to use as overlays both for the volume or 
the surface. Is this what you mean?

On 10/28/16 9:17 AM, Eloy Geenjaar wrote:

Dear Freesurfer Experts,


I am a student at the technical university of Delft and currently working on a 
project to automatically visualize the cortical thickness data of children. To 
automatically visualize the data I want to use Freeview, to use Freeview as 
visualization tool I have to write brain specific layout files. To do this 
automatically I want to know what the layout for the overlay files is, so 
Freeview can read them automatically. The data for the layout files should be 
different per brain, I have already acquired the data and I am ready to write 
it to a layout file, but I can't figure out what the standard way of writing a 
layout file is, without having to manually do anything. The language in which I 
want to write the code is Python.


Kind regards,


Eloy Geenjaar



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

___
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] Two Stage Longitudinal Model

[Freesurfer] Longitudinal analysis

Re: [Freesurfer] Amygdala subfields

Re: [Freesurfer] fsaverage_sym LR-flipchecks

Re: [Freesurfer] Creating overlay files automatically

Re: [Freesurfer] Recon-all Exiting without Error

Re: [Freesurfer] Amygdala subfields

Re: [Freesurfer] values of 0 in the beta.mgh files

Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

[Freesurfer] Amygdala subfields

Re: [Freesurfer] Obtain images extracted from aseg.mgz that have been corrected for partial volume effects

Re: [Freesurfer] Recon-all Exiting without Error

[Freesurfer] Recon-all Exiting without Error

Re: [Freesurfer] Extend pial surface

Re: [Freesurfer] [Question for recommended MRI protocols]

Re: [Freesurfer] values of 0 in the beta.mgh files

[Freesurfer] recon-all steps question

Re: [Freesurfer] Creating overlay files automatically

18 matches

Site Navigation

Mail list logo

Footer information