[Freesurfer] Can MRIread function read .mgz file

[chenhf_uestc]

Dear Freesurfer expert,

How could I read the .mgz file into Matlab, the online manual FAQ stated

Q. Can I load FreeSurfer output in Matlab?
A: If you write it as .mgz format then load_mgh (or MRIread) will read it. 
In addition, in the MRIread function, it stated that
% mri = MRIread(fstring,headeronly)
%
% Reads in a volume based on the fstring. fstring can be:
%  1. A stem, in which case the format and full file name is determined
% by finding a file on disk called fstring.ext, where ext can be
% either mgh, mgz, img, bhdr, nii, or nii.gz
%  2. MGH file. Eg, f.mgh or f.mgz
However, I cannot read the .mgz file using MRIread
A = mriread('lh.thickness.20.mgz');
??? SWITCH expression must be a scalar or string constant.

Error in ==> load_mgh at 158
switch type

Error in ==> MRIread at 87
  [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);

If this function cannot read the .mgz file, how can I read it?

Best,
Feng


2015-09-17


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[Freesurfer] slope_age.mtx unknown

[stdp82]

Hi list,I'm performing one group and one covariate on resting state FAST 
analysis.Here, I'm reporting the error.ThanksBest regards,
Stefano
mri_glmfit --glmdir my-glm_age.wls --y y.mgh --nii.gz --fsgd file_age.fsgd --C 
intercept_age.mtx —-C slope_age.mtx
gdfReadHeader: reading file_age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 62.6667 8.25967
Class Means of each Continuous Variable
1 Main  62.6667 
INFO: gd2mtx_method is dods
ERROR: Option slope_age.mtx unknown
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Eugenio Iglesias]

Hi Priyanka,
in the mri directory of each subject, you will find a file named:
[lr]h.hippoSfLabels--.v10.1mm.mgz
which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel 
space of that subject. 
Kind regards,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Priyanka Mehta" 
To: "Freesurfer support list" 
Sent: Sunday, September 13, 2015 10:14:34 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Hi again 

I want to use my hippocampal segmentation for masking 2380 brain volumes. Is 
there a way to find out using Freesurfer if the hippocampal subfields and the 
2380 volumes are in the same space? The mean of the 2380 volumes and the 
hippocampal subfields align correctly when I use Freesurfer's freeview to view 
them. But does that also mean they are in the same voxel space? 

And if they aren't in the same space, is there any way using Freesurfer that I 
can have the two in the same space? 

I really appreciate any suggestions! 

Thanks, 
Priyanka Mehta 

On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > 
wrote: 


of course 
On Tue, 25 Aug 2015, Priyanka wrote: 

> Thanks Bruce. Just wanted to make sure I've got the correct output. 
> 
> Really appreciate the help. 
> 
> Thanks again, 
> Priyanka Mehta 
> 
>> On Aug 25, 2015, at 4:44 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > 
>> wrote: 
>> 
>> Hi Priyanka 
>> 
>> that is what mri_extract_label is designed to do. This facilitates making 
>> density maps in a common space. If you want to get the original label # back 
>> you can use something like: 
>> 
>> mri_binarize --match 128 --binval  or something like that 
>> 
>> cheers 
>> Bruce 
>> 
>> 
>>> On Tue, 25 Aug 2015, Priyanka Mehta wrote: 
>>> 
>>> Reposting my question: 
>>> This happens for all the segments that I've tried to extract using 
>>> mri_extract_label. They all show up as 128 nerve after mri_extract_label. 
>>> Is 
>>> this a bug in the dev version? 
>>> Any help is greatly appreciated! 
>>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka < priyankamehta0...@gmail.com > 
>>> wrote: 
>>> This happens for all the segments that I've tried to extract 
>>> using mri_extract_label. They all show up as 128 nerve after 
>>> mri_extract_label. Is this a bug in the dev version? 
>>> 
>>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell 
>>> < ltirr...@nmr.mgh.harvard.edu > wrote: 
>>> > 
>>> > It seems that the command: 
>>> > 
>>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii 
>>> > 
>>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 
>>> in lh.hippoSfLabels-T1.v10.mgz. You can run: 
>>> > 
>>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii 
>>> > 
>>> > and then the correct label names from the Lookup Table will 
>>> show up. 
>>> > 
>>> > Best, 
>>> > Lee 
>>> > 
>>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: 
>>> >> 
>>> >> Hi Eugenio 
>>> >> Thank you for the explanation, it makes sense to me now. 
>>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it 
>>> aligns correctly. However, when I view the segmentation 
>>> >> with color map set to Lookup Table and 'show existing labels 
>>> only' checked, the lh.CA1.nii segment shows as 128 Nerve 
>>> >> label. Shouldn't it still be showing up as 206 CA1 label? I 
>>> am confused. 
>>> >> 
>>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias 
>>> < e.igles...@bcbl.eu > wrote: 
>>> >> Hi Prya, 
>>> >> that is because MriCron is not that great at overlaying 
>>> images that are in the same physical space but not 
>>> >> in the same voxel space. You have two options here: 
>>> >> 1. Use FreeSurfer's Freeview rather than MriCron to 
>>> visualize the output. FreeView will correctly overlay 
>>> >> the segmentation. 
>>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than 
>>> lh.hippoSfLabels-T1.v10.mgz) when you call 
>>> >> mri_extract_label. That volume lives in the same voxel 
>>> space as T1.nii, and should be properly overlayed 
>>> >> by MriCron. However, the resolution of the segmentation 
>>> will be 1 mm, rather than the 0.333 mm that you'd 
>>> >> get in option 1. 
>>> >> Cheers, 
>>> >> Eugenio 
>>> >> 
>>> >> Juan Eugenio Iglesias 
>>> >> Postdoctoral researcher BCBL 
>>> >> www.jeiglesias.com 
>>> >> www.bcbl.eu 
>>> >> 
>>> >> Legal disclaimer/Aviso legal/Lege-oharra: 
>>> www.bcbl.eu/legal-disclaimer 
>>> >> 
>>> >> - Original Message - 
>>> >> From: "Priyanka Mehta" < priyankamehta0...@gmail.com > 
>>> >> To: "Freesurfer support list" 
>>> < freesurfer@nmr.mgh.harvard.edu > 
>>> >> Sent: Wednesday, August 19, 2015 7:50:12 PM 
>>> >> Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version 
>>> Output 
>>> >> 
>>> >> Hi 
>>> >> 
>>> >> This is a follow-up question to my previous problem. 
>>> >> After I 

[Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0

[Carl Pintzka]

Hi,


We are currently planning a population based MRI study and are interested in 
including a T2w scan that allows us to perform the new automatic hippocampal 
subfield segmentation included in Freesurfer 6.0.


The current scanner settings (which has been used in a previous study) are as 
follows:


3T Siemens Skyra

T2w turbo spin echo

TR: 6760, TE: 84

In plane resolution: 0.57x0.57mm

Slice thickness: 1mm, no gap

NAX: 3


In the Iglesias 2015 paper, 0.4x0.4 in plane resolution with 2mm slice 
thickness is used. Is this preferable since we intend on using the subfield 
segmentation on our dataset, or is it ok with 0.57x0.57 in plane resolution and 
thinner slices? We are not planning on performing manual segmentation on the 
dataset and thus want the settings to be optimal for the Freesurfer 
segmentation.


What about number of averages?


Best regards,


Carl Pintzka
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Re: [Freesurfer] License issue with qdec

[Douglas N Greve]

did you recently upgrade or reinstall? Does anything else run since you 
found this problem? Eg, mri_convert? When you created the .license file, 
did you put a valid license key in it?

On 09/17/2015 12:09 PM, Lisa S. Pao wrote:
> Hi everyone,
>
> I’m having some issues using qdec. The program runs for about 30 
> seconds, and then quits with the following error message:
>
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not 
> found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
>
> I’ve been using Freesurfer for over a year now to run recons and use 
> freeview, so I’m not sure why the error is popping up now. I 
> definitely have a license, and have successfully used the program (but 
> not qdec) in the past.
>
> I’ve tried the following fixes without any success:
> -renaming the ‘license.txt’ file to ‘license’ (without the .txt 
> extension)
> -using terminal to create a file called ‘.license’ (when I did this 
> and used ls -a to view all files, I noticed the file was actually 
> named ‘.license.save’)
>
> I’m running freesurfer-i386-apple-darwin11.4.2-stable5-20130514 on an 
> iMac, OS X Yosemite (10.10.3).
>
> I’d greatly appreciate any suggestions for how to fix this issue.
>
> Thanks!
>
> Best,
> Lisa
>
> ---
> Lisa Pao, Ph.D.
> Postdoctoral Research Fellow
> Division of Child and Adolescent Psychiatry
> Columbia University Medical Center
> New York State Psychiatric Institute
> 646-774-5782
>
>
>
>
>
> ___
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-- 
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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[Freesurfer] License issue with qdec

[Lisa S. Pao]

Hi everyone,

I’m having some issues using qdec. The program runs for about 30 seconds, and 
then quits with the following error message:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

I’ve been using Freesurfer for over a year now to run recons and use freeview, 
so I’m not sure why the error is popping up now. I definitely have a license, 
and have successfully used the program (but not qdec) in the past.

I’ve tried the following fixes without any success:
-renaming the ‘license.txt’ file to ‘license’ (without the .txt extension)
-using terminal to create a file called ‘.license’ (when I did this and used ls 
-a to view all files, I noticed the file was actually named ‘.license.save’)

I’m running freesurfer-i386-apple-darwin11.4.2-stable5-20130514 on an iMac, OS 
X Yosemite (10.10.3).

I’d greatly appreciate any suggestions for how to fix this issue.

Thanks!

Best,
Lisa

---
Lisa Pao, Ph.D.
Postdoctoral Research Fellow
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
646-774-5782



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Re: [Freesurfer] How to handle the termination of recon-all after mris_remove_intersection

[Bruce Fischl]

Hi,

you should copy the list on this type of email so others can answer.

Bruce

On Thu, 17 Sep 2015, Nakyoung Kim wrote:


oops, I didn't notice there's a cp after mris_remove_intersection.
Thanks for your advice.

I found a small error in recon-all script as follows:




  # run surface intersection checker/fixer
  foreach hemi ($hemilist)
    set xopts = `fsr-getxopts mris_remove_intersection $XOptsFile`;
    set cmd = (mris_remove_intersection)




should be changed like this.




  # run surface intersection checker/fixer
  foreach hemi ($NewTopoFixHemiList)
  set xopts = `fsr-getxopts mris_remove_intersection $XOptsFile`;
  set cmd = (mris_remove_intersection)




Is this OK?


Thank you in advance,
Nakyoung Kim.

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[Freesurfer] Fwd: OHBM Glass Brain Award: Nomination Deadline November 9th

[Douglas N Greve]

 Forwarded Message 
Subject:OHBM Glass Brain Award: Nomination Deadline November 9th
Date:   Thu, 17 Sep 2015 09:37:55 -0500
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu



*ORGANIZATION FOR HUMAN BRAIN MAPPING *
**GLASS BRAIN AWARD**
/A lifetime achievement award in the field of human brain mapping/

Dear OHBM Member,

The Organization for Human Brain Mapping Council has established an 
award to recognize lifetime achievement by leading researchers using or 
facilitating neuroimaging to discover original and influential findings 
regarding the organization and function of the human brain today.

*Award Criteria*

 1. Nominee must have been visibly engaged in OHBM activities
 2. Nominee must have evidence of extraordinary lifetime accomplishments
in the field of human brain mapping
 3. The nominee must be over the age of 40
 4. The nominee must be present to accept the award given out at the
22nd Annual Meeting of the Organization for Human Brain Mapping
being held June 26-30, 2016 in Geneva, Switzerland
 5. No self-nominations are allowed

*Nomination Process*
Nominations for the Glass Brain Award should include a letter of 
nomination outlining the nominee’s lifetime accomplishments as well as 
an abbreviated curriculum vita (no more than 2 pages) of the nominee. 
Additional letters of support are not required but may add to the 
strength of the nomination.  Nominators are required to collate all 
nomination materials into one single PDF document (no more than 5 pages 
total) to be emailed to OHBM at i...@humanbrainmapping.org 
. *Please limit the nomination 
materials to 5 pages.  Deadline for nominations is November 9, 2015.*

*Review Process*
The OHBM Council is charged with the selection of the Glass Brain Award 
recipient and will meet after the submission deadline to review the 
award criteria and discuss each nominee. The Council will then vote 
electronically on their top ranked candidates.  If needed, the Council 
will meet again to discuss any split decisions and make a final 
selection.  The award recipient will be notified in April. The award 
recipient will not be announced until the Opening Ceremonies at the 
Annual Meeting.

*Award*
The award recipient will be provided with an OHBM Glass Brain Award, 
gratis Annual Meeting registration, coach travel and two nights lodging 
at the host hotel.

We look forward to your involvement in the nomination process.  Please 
contact the OHBM Executive Office at i...@humanbrainmapping.org 
 with any questions.

Sincerely,

JoAnn Taie
Executive Director
Organization for Human Brain Mapping (OHBM)





*Save the Date!
June 26-30, 2016* 


*2015  Glass
Brain Recipient
Marcus E. Raichle, MD*

*2014 Glass
Brain Recipient
Karl Zilles, MD, PhD*



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Re: [Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0

[Eugenio Iglesias]

Hi Carl,
this is hard to say in advance. Do you see the internal band (the "swiss roll" 
or "dark band") of the hippocampus in your scans? If so, then I would go for 
it. If not, I would trade a bit of slice separation for in-plane resolution.
If you want, feel free to send me a capture of a representative coronal slice 
in the hippocampal body.
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Carl Pintzka" 
To: "Freesurfer support list" 
Sent: Thursday, September 17, 2015 2:50:23 PM
Subject: [Freesurfer] Scanner parameters for hippocampal subfield segmentation 
in Freesurfer 6.0

Hi, 





We are currently planning a population based MRI study and are interested in 
including a T2w scan that allows us to perform the new automatic hippocampal 
subfield segmentation included in Freesurfer 6.0. 





The current scanner settings (which has been used in a previous study) are as 
follows: 





3T Siemens Skyra 

T2w turbo spin echo 

TR: 67 60, TE: 84 


In plane resolution: 0.57x0.57mm 


Slice thickness: 1mm, no gap 


NAX: 3 



In the Iglesias 2015 paper, 0.4x0.4 in plane resolution with 2mm slice 
thickness is used. Is this preferable since we intend on using the subfield 
segmentation on our dataset, or is it ok with 0.57x0.57 in plane resolution and 
thinner slices? We are not planning on performing manual segmentation on the 
dataset and thus want the settings to be optimal for the Freesurfer 
segmentation. 





What about number of averages? 





Best regards, 





Carl Pintzka 

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Re: [Freesurfer] Can MRIread function read .mgz file

[Bruce Fischl]

Hi Feng

can you load that file into tksurfer/freeview? It sounds like something 
is wrong with it. You should also just run ls -l on it and see if it looks 
reasonable in terms of size and permissions


cheers
Bruce

On Thu, 17 Sep 2015, chenhf_uestc wrote:


Dear Freesurfer expert,
 
How could I read the .mgz file into Matlab, the online manual FAQ stated
 
Q. Can I load FreeSurfer output in Matlab?

A: If you write it as .mgz format then load_mgh (or MRIread) will read it.

In addition, in the MRIread function, it stated that

% mri = MRIread(fstring,headeronly)
%
% Reads in a volume based on the fstring. fstring can be:
%  1. A stem, in which case the format and full file name is determined
% by finding a file on disk called fstring.ext, where ext can be
% either mgh, mgz, img, bhdr, nii, or nii.gz
%  2. MGH file. Eg, f.mgh or f.mgz

However, I cannot read the .mgz file using MRIread

A = mriread('lh.thickness.20.mgz');
??? SWITCH expression must be a scalar or string constant.
 
Error in ==> load_mgh at 158
switch type
 
Error in ==> MRIread at 87
  [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
 
If this function cannot read the .mgz file, how can I read it?
 
Best,
Feng
 
 
2015-09-17


chenhf_uestc

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Re: [Freesurfer] Tracula mean path

[Peggy Skelly]

The mean path points look oriented correctly in the 5.3 stable version of
Freeview. I downloaded and tested the latest dev version for my platform
(freesurfer-Darwin-lion-dev.tar.gz - dated 2015-08-22), and the path points
are not correct (orientation is rotated).

Peggy

On Tue, Sep 15, 2015 at 11:15 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Peggy - Dec 19 2014 sounds like it was built after the 5.3 release. Can
> you try with the 5.3 version of freeview?
>
> a.y
>
> On Tue, 15 Sep 2015, Peggy Skelly wrote:
>
> I think it's the one that came with 5.3 stable release (but maybe not - I
>> did download a dev version at one
>> time, but I don't recall replacing the Freeview.app file. But my memory
>> isn't what it once was ;)). I'm
>> using freesurfer-Darwin-lion-stable-pub-v5.3.0. Freeview.app is 129 MB
>> and it's About box says it's Version
>> 1.0 Build Dec 19 2014 16:29:56.
>> Peggy
>>
>> On Tue, Sep 15, 2015 at 5:08 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Peggy - Are you by any chance using the development version of
>> freeview? Or are you using the
>>   one that came with the 5.3 release?
>>
>>   a.y
>>
>>   On Tue, 15 Sep 2015, Peggy Skelly wrote:
>>
>> HI,
>> I'm looking at the mean path output from the tracula
>> tutorial. I ran 'trac-all
>> -stat' on the tutorial data and examined the output in
>> freeview along
>> with $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz. My mean paths
>> appear to be rotated 90° relative to what they should be:
>> Inline image 1
>>
>> What could have gone wrong?
>>
>> Thanks,
>> Peggy
>>
>>
>>   ___
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>>
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Re: [Freesurfer] Segmentation in dev version

[Lee Tirrell]

Hi Priyanka,

The cortical labels are exactly the same for wmparc.mgz and the aparc+aseg.mgz, 
they just differ in how they label the subcortical structures and white matter. 
It should matter which you use for masking the cortex.


The "_exvivo" in the label names is new to the dev version of Freesurfer, I 
previously answered your question based on the output from Freesurfer 5.3.  I 
looked at a subject processed with dev, and it seems there are are 
?h.perirhinal_exvivo.label files in the label directory and a 
?h.BA_exvivo.stats file in the stats directory. The perirhinal cortex should 
also be included in the ?h.BA_exvivo.annot files.


If the stats file is missing, you can extact them from the ?h.BA_exvivo.annot 
files using the following commands:


cd $SUBJECTS_DIR/subject_name/label
mris_anatomical_stats -mgz -f ../stats/lh.BA_exvivo.stats -b -a 
./lh.BA_exvivo.annot -c ./BA_exvivo.ctab subject_name lh white
mris_anatomical_stats -mgz -f ../stats/rh.BA_exvivo.stats -b -a 
./rh.BA_exvivo.annot -c ./BA_exvivo.ctab subject_name rh white

Also, if this doesn't work, I can send you the perirhinal label from fsaverage, 
and you can map this to your subject using mri_label2label.


Best,
Lee



On Thu, 10 Sep 2015, Priyanka Mehta wrote:


Correction in the previous message: I need to mask the functional images (EPI) 
for further analysis.

On Wed, Sep 9, 2015 at 11:56 PM, Priyanka Mehta  
wrote:
  Thank you for the explanation Lee.
I need to use the cortical labels for masking the T1 for further analysis. 
Which file should I be using then - wmparc.mgz or aparc+aseg.mgz?

For the perirhinal cortex, I do not have the following files even after running 
recon-all
/label/lh.BA.annot
/label/rh.BA.annot

/stats/lh.BA.stats
/stats/rh.BA.stats

Instead I have these files (The .stats files are missing):
/label/lh.BA_exvivo.annot
/label/rh.BA_exvivo.annot

Your help is greatly appreciated!

Priyanka Mehta


On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell  
wrote:
  Hi Priyanka,

  The cortical labels are the same for wmparc.mgz and aparc+aseg.mgz (taken 
from the ?h.aparc.annot files), but they differ on the way the white matter is 
labeled. The aparc+aseg uses the white matter and subcortical
  labels from the aseg.mgz, while the wmparc labels each point in the white 
matter as the nearest cortical label to that point, as well as the subcortical 
labels from the aseg.

  The perirhinal cortex isn't included in the aparc, so it isn't in either 
of these mgz files.  However, it is included in the Brodmann area annotation 
files, and stats are computed for this region automatically when
  you run recon-all:

  /label/lh.BA.annot
  /label/rh.BA.annot

  /stats/lh.BA.stats
  /stats/rh.BA.stats


  To see this on the inflated left hemisphere, for example, you can run:

  freeview -f subject/surf/lh.inflated:annot=subject/label/lh.BA.annot

  Best,
  Lee


  On Thu, 20 Aug 2015, Priyanka Mehta wrote:

Hi Lee

Thank you for your response.
I have a follow up question- After running recon-all -all, I found 
the parahippocampal cortex and entorhinal cortex under two files- wmparc.mgz 
and aparc+ages.mgz. What is the difference between the two?
Also, I haven't been able to find perirhinal cortex under any of 
the files. I wonder why?



On Mon, Aug 3, 2015 at 5:22 PM, Lee Tirrell 
 wrote:
      Hi Priyanka,

      These are all automatically created automatically by running 
recon-all -all.

      Best,
      Lee

      On Sat, 1 Aug 2015, Priyanka Mehta wrote:

            Hi
            Please excuse my extremely basic question.

            I would like to perform segmentation on my T1 image to 
obtain the following:

            a. Entorhinal Cortex

            b. Perirhinal Cortex

            c. Parahippocampal Cortex

            Is there a specific command I should be using in the 
6.0 dev version? Or should I just be using recon-all -all ?

            Best,
            Priyanka Mehta
             


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[Freesurfer] fast_selxavg3() failed\n

[stdp82]

Hi list,
I'm performing FS-FAST on rsfMRI.The seed is MRS voxel.I have run:
1-mri_convert MRS_MASK.nii.gz $SUBJECTS_DIR/MRS_MASK.mgz 
2-fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg 
mean.MRS_MASK.config
3-fcseed-sess -sf sessid -cfg mean.MRS_MASK.config
4-  mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh 
-fwhm 5 -notask -taskreg MRS_MASK.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
-polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run  mkanalysis-sess 
-analysis fc.MRS_MASK.surf.rh -surface fsaverage rh -fwhm 5 -notask -taskreg 
MRS_MASK.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 
-mcextreg -fsd rest -TR 1.1 -per-run  mkanalysis-sess 
-analysis fc.MRS_MASK.mni305 -mni305 -fwhm 5 -notask -taskreg MRS_MASK.dat 1 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5  -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.1 -per-run
5-  selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh selxavg3-sess -sf 
sessid -a fc.MRS_MASK.surf.rh selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305
When I performed selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh
I obtained this error:
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer/matlab/MRIread.m
-
outtop = /Applications/freesurfer/subjects
Extension format = nii.gz
ERROR: cannot find volume matching 
/Applications/freesurfer/subjects/Sess101/rest/001/MRS_MASK.dat
ERROR: loading nonpar reg 
/Applications/freesurfer/subjects/Sess101/rest/001/MRS_MASK.dat
--
ERROR: fast_selxavg3() failed\n
PLEASE NOTE: MRS_MASK.dat is lacking in Sess101/rest/001. It is present only 
MRS_MASK without extension.
Thanks,

Stefano
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Re: [Freesurfer] pial_lgi option in qdec

[Marie Schaer]

Tara,

After copying the .Qdecrc, did you check that the .Qdecrc file is in your home 
directory and that MEASURE1 = pial_lgi is listed there? When this is fine, 
start with a new terminal and pial_lgi should be in the option among other 
measures.

Let me know,

Marie


On Sep 17, 2015, at 4:02 PM, Tara Miskovich 
>
 wrote:

Hi all,

I just transferred data from a drive to do some LGI analyses, and all the data 
has already been processed and cached, so I have all the results sample to the 
fsaverage at various levels of smoothing for each subject.

Additionally, I added the .Qdecrc file so pial_lgi would pop up as an option, 
but that did not seem to work. Does anyone know what might be going on, and how 
I can get that option to pop up in qdec?

--
Thank you,

Tara
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Re: [Freesurfer] pial_lgi option in qdec

[Tara Miskovich]

Thank you for the response Marie. By home directory do you mean the
freesurfer home directory? Currently, I have it in the qdec directory as
stated in the wiki and it appears to be correct.

Thanks again,
Tara

On Thu, Sep 17, 2015 at 6:09 PM, Marie Schaer  wrote:

>
> Tara,
>
> After copying the .Qdecrc, did you check that the .Qdecrc file is in your
> home directory and that MEASURE1 = pial_lgi is listed there? When this is
> fine, start with a new terminal and pial_lgi should be in the option among
> other measures.
>
> Let me know,
>
> Marie
>
>
> On Sep 17, 2015, at 4:02 PM, Tara Miskovich 
>  wrote:
>
> Hi all,
>
> I just transferred data from a drive to do some LGI analyses, and all the
> data has already been processed and cached, so I have all the results
> sample to the fsaverage at various levels of smoothing for each subject.
>
> Additionally, I added the .Qdecrc file so pial_lgi would pop up as an
> option, but that did not seem to work. Does anyone know what might be going
> on, and how I can get that option to pop up in qdec?
>
> --
> Thank you,
>
> Tara
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-- 
Thank you,

Tara A. Miskovich, M.S.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uwm.edu
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[Freesurfer] pial_lgi option in qdec

[Tara Miskovich]

Hi all,

I just transferred data from a drive to do some LGI analyses, and all the
data has already been processed and cached, so I have all the results
sample to the fsaverage at various levels of smoothing for each subject.

Additionally, I added the .Qdecrc file so pial_lgi would pop up as an
option, but that did not seem to work. Does anyone know what might be going
on, and how I can get that option to pop up in qdec?

-- 
Thank you,

Tara
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Re: [Freesurfer] pial_lgi option in qdec

[Marie Schaer]

Hi Tara,

Try in your home directory as well (i.e. where you land where you put only cd 
on the command line), sometimes if it doesn't work from the qdec directory this 
will do it. And then open a new terminal and start qdec.

Keep me posted!

Marie

On Sep 17, 2015, at 4:26 PM, Tara Miskovich 
>
 wrote:

Thank you for the response Marie. By home directory do you mean the freesurfer 
home directory? Currently, I have it in the qdec directory as stated in the 
wiki and it appears to be correct.

Thanks again,
Tara

On Thu, Sep 17, 2015 at 6:09 PM, Marie Schaer 
> wrote:

Tara,

After copying the .Qdecrc, did you check that the .Qdecrc file is in your home 
directory and that MEASURE1 = pial_lgi is listed there? When this is fine, 
start with a new terminal and pial_lgi should be in the option among other 
measures.

Let me know,

Marie


On Sep 17, 2015, at 4:02 PM, Tara Miskovich 
>
 wrote:

Hi all,

I just transferred data from a drive to do some LGI analyses, and all the data 
has already been processed and cached, so I have all the results sample to the 
fsaverage at various levels of smoothing for each subject.

Additionally, I added the .Qdecrc file so pial_lgi would pop up as an option, 
but that did not seem to work. Does anyone know what might be going on, and how 
I can get that option to pop up in qdec?

--
Thank you,

Tara
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--
Thank you,

Tara A. Miskovich, M.S.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uwm.edu
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Re: [Freesurfer] pial_lgi option in qdec

[Tara Miskovich]

That did it! Thank you!

Tara

On Thu, Sep 17, 2015 at 6:33 PM, Marie Schaer  wrote:

>
> Hi Tara,
>
> Try in your home directory as well (i.e. where you land where you put only
> cd on the command line), sometimes if it doesn't work from the qdec
> directory this will do it. And then open a new terminal and start qdec.
>
> Keep me posted!
>
> Marie
>
> On Sep 17, 2015, at 4:26 PM, Tara Miskovich 
>  wrote:
>
> Thank you for the response Marie. By home directory do you mean the
> freesurfer home directory? Currently, I have it in the qdec directory as
> stated in the wiki and it appears to be correct.
>
> Thanks again,
> Tara
>
> On Thu, Sep 17, 2015 at 6:09 PM, Marie Schaer 
> wrote:
>
>>
>> Tara,
>>
>> After copying the .Qdecrc, did you check that the .Qdecrc file is in your
>> home directory and that MEASURE1 = pial_lgi is listed there? When this is
>> fine, start with a new terminal and pial_lgi should be in the option among
>> other measures.
>>
>> Let me know,
>>
>> Marie
>>
>>
>> On Sep 17, 2015, at 4:02 PM, Tara Miskovich 
>>  wrote:
>>
>> Hi all,
>>
>> I just transferred data from a drive to do some LGI analyses, and all the
>> data has already been processed and cached, so I have all the results
>> sample to the fsaverage at various levels of smoothing for each subject.
>>
>> Additionally, I added the .Qdecrc file so pial_lgi would pop up as an
>> option, but that did not seem to work. Does anyone know what might be going
>> on, and how I can get that option to pop up in qdec?
>>
>> --
>> Thank you,
>>
>> Tara
>> ___
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>> 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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>> is
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>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Thank you,
>
> Tara A. Miskovich, M.S.
> Affective Neuroscience Laboratory
> Department of Psychology
> University of Wisconsin-Milwaukee
> 334 Garland Hall
> misko...@uwm.edu
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-- 
Thank you,

Tara A. Miskovich, M.S.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uwm.edu
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Re: [Freesurfer] How to handle the termination of recon-all after mris_remove_intersection

[Nakyoung Kim]

oops, I didn't notice there's a cp after mris_remove_intersection.



Thanks for your advice.



I found a small error in recon-all script as follows:









  # run surface intersection checker/fixer

  foreach hemi ($*hemilist*)

set xopts = `fsr-getxopts mris_remove_intersection $XOptsFile`;

set cmd = (mris_remove_intersection)









should be changed like this.









  # run surface intersection checker/fixer

  foreach hemi ($*NewTopoFixHemiList*)

  set xopts = `fsr-getxopts mris_remove_intersection $XOptsFile`;

  set cmd = (mris_remove_intersection)









Is this OK?





Thank you in advance,

Nakyoung Kim.
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