date:20151030

[Freesurfer] bring volumes to fsaverage space

2015-10-30 Thread Shani Ben Amitay

Dear freesurfers,

I would like to know what will be the best way to bring volumes in the
individual subject's space  to the fsaverage space.

Thanks,
Shani
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[Freesurfer] error vcsf.config

2015-10-30 Thread stdp82

Hi list,
During fcseed-sess -s subj -cfg vcsf.config
a subject produces the follow error.I have rerun recon-all, cheched aparc+aseg 
with tkmedit. They seem to be ok.Why this error is produced?
Thanks

Stefano

Creating output directory 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm
Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz
Saving design matrix to 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat
Normalized matrix condition is 61.5872
Matrix condition is 1e+08
Pruning voxels by thr: 0.00
Found 0 voxels in mask
Saving mask to 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh
search space = 0.00
DOF = 297
Starting fit and test
Fit completed in 0.0008 minutes
Computing temporal AR1
Writing results
Computing FSNR
  mean
maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
  linear
maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
  quad
maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
Computing PCA (300)
ERROR: no voxels in mask___
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[Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

2015-10-30 Thread Knut Jørgen Bjuland


Hi

When I start freeview form command line on Mac OS X 11.10 it crash with this 
error message. Do I miss a file?


freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: 
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: 
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 5 TRAP
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by 
knutjorgenbjulan Fri Oct 30 09:42:53 2015
[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 
FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

Knut Jørgen Bjuland
NTNU___
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[Freesurfer] average z-score of each subject from a common cluster

2015-10-30 Thread stdp82

Hi list,I have two queries, please.
I'd like to have the z-score from my rsfMRI data (seed-analyis).
1) I have extract the z-score from the Vtx Max
In details, after groups comparison analysis, I have opened the 
cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have 
read the Vtx Max coordinates.Next, I have open the z.nii.gz of each subject and 
I have expected the z-score from the vertex which have the Vtx Max coordinates.
Is this procedure corrected?
2) z-score of each subject from a common cluster
I would like to use the cluster which shows the group difference 
(cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract from it 
the average of the z-score which is contained in each subject.How should I do? 
Thanks.

Stefano
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[Freesurfer] Tracula stats COR-.info does not exist

2015-10-30 Thread Simon Jones

Dear Tracula developers,

 

I posted a problem with tracula when I ran

trac-all -stat -c  dmrirc_ind_mni_cvs_all_stats.all

 

I receive this error message

 

Loading output reference volume from

/home/spj24/app/freesurfer/subjects/cvs_avg35

 

corRead(): can't open file

/home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info

 

ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35

There is no file called COR-.info in the directory

/home/spj24/app/freesurfer/subjects/cvs_avg35/

 

I have now changed the lines in the configuration file

 

set doregcvs = 1
 
# CVS template subject ID
# Only used if doregcvs = 1
# Default: cvs_avg35
#
#set cvstemp = donald
set cvstemp = cvs_avg35
 
set cvstempdir = $FREESURFER_HOME/subjects
 
to
 
set doregcvs = 1
set cvstemp = cvs_avg35/mri/brainmask.mgz
set cvstempdir = $FREESURFER_HOME/subjects

 

i.e. explicitly pointing to an image in the cvs_avg35 directory and the
stats seem to complete without error.

 

Is that the right thing to do?

 

Thanks for your help,

 

Simon

 

 

 

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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

2015-10-30 Thread Bruce Fischl

what is the laus250 parcellation? The lookup tables are in text so you 
should be able to open one in an editor and see what the format is. It's 
pretty straightforward. # lines are comments, then it is

cheers
Bruce

On Fri, 30 Oct 2015, Peled, Noam wrote:

> Hey all,
> I used mri_aparc2aseg to map the cortical labels from the laus250 
> parcellation.
> Now I need to create a new lookup table, mainly for displaying the labels' 
> names in freeview.
> How can I know what id each label gets in my new laus+aseg.mgz file?
>
> Thanks,
> Noam
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>
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Re: [Freesurfer] bring volumes to fsaverage space

2015-10-30 Thread Bruce Fischl


Hi Shani

you can use mri_vol2vol with the talairach.m3z. Alternatively, you can 
run CVS which will give you more accurate cortical matching and use the 
transform that it produces.


cheers
Bruce
On Fri, 30 Oct 2015, Shani Ben Amitay wrote:


Dear freesurfers,
I would like to know what will be the best way to bring volumes in the
individual subject's space  to the fsaverage space.

Thanks, 
Shani

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Re: [Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

2015-10-30 Thread Z K

There are significant changes in the most recent OSX release El Capitan 
and this is one consequence of them 
(https://en.wikipedia.org/wiki/OS_X_El_Capitan#System_Integrity_Protection). 
We are currently exploring solutions but as of right now, freesurfer is 
not fully functional on OS X 10.11



On 10/30/2015 04:45 AM, Knut Jørgen Bjuland wrote:
>
> Hi
>
>
> When I start freeview form command line on Mac OS X 11.10 it crash with
> this error message. Do I miss a file?
>
>
>
> freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>
>Referenced from:
> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>
>Expected in: /usr/lib/libSystem.B.dylib
>
>
> dyld: Symbol not found: ___emutls_get_address
>
>Referenced from:
> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>
>Expected in: /usr/lib/libSystem.B.dylib
>
>
> [0]PETSC ERROR:
> 
>
> [0]PETSC ERROR: Caught signal number 5 TRAP
>
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
>
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [0]PETSC ERROR: to get more information on the crash.
>
> [0]PETSC ERROR: - Error Message
> 
>
> [0]PETSC ERROR: Signal received!
>
> [0]PETSC ERROR:
> 
>
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>
> [0]PETSC ERROR: See docs/index.html for manual pages.
>
> [0]PETSC ERROR:
> 
>
> [0]PETSC ERROR: Unknown Name on a darwin12. named
> Knuts-MacBook-Pro.local by knutjorgenbjulan Fri Oct 30 09:42:53 2015
>
> [0]PETSC ERROR: Libraries linked from
> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
>
> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
>
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>
> [0]PETSC ERROR:
> 
>
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
>
> [unset]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
> Knut Jørgen Bjuland
> NTNU
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

2015-10-30 Thread Emad Ahmadi

Hi Freesurfer experts,

I hope you’re all enjoying your day!

Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms 
obtained at Martinos Center. The dicoms have the following format:

MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919
MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196
MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464
...

I receive error when I run dcm2niix (to extract the b values and b vectors): 

Command:
dcm2niix -f dti 

The error I receive:

Warning: output folder invalid 
MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try 
Error: unable to find any DICOM images in 
Conversion required 0.00 seconds.

When I do the following steps to generate “treatable” dicoms, dcm2niix 
recognizes these dicoms:

1. copy Martinos Center dicoms to my local Mac
2. import dicoms into OsiriX
3. Export them as dicoms
4. copy the OsiriX-exported dicoms back to Launchpad
5. Run dcm2niix on the new dicoms

Since this copying back and forth takes a lot of time, I need a better way to 
convert the “crazy” Martinos Center dicoms into the “treatable” ones!

I would really appreciate your help.

Best,
Emad


Emad Ahmadi, MD
---
Research Fellow
Department of Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

2015-10-30 Thread dgw

Hi Emad,

The only problems, which I have run into is major weaknesses in dcm2nii:
1. You must have write permissions on the directory the files are 
located in.
2. dcm2nii cannot work on symbolically linked files.

Therefore, first copy the files to your own analysis workspace: e.g. 
/cluster//
then run dcm2nii.
With that I have no problems.

hth
d

On 10/30/15 10:28 AM, Emad Ahmadi wrote:
> Hi Freesurfer experts,
>
> I hope you’re all enjoying your day!
>
> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms
> obtained at Martinos Center. The dicoms have the following format:
>
> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919
> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196
> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464
> ...
>
> I receive error when I run dcm2niix (to extract the b values and b
> vectors):
>
> Command:
> dcm2niix -f dti 
>
> The error I receive:
>
> Warning: output folder invalid
> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try
> Error: unable to find any DICOM images in
> Conversion required 0.00 seconds.
>
> When I do the following steps to generate “treatable” dicoms, dcm2niix
> recognizes these dicoms:
>
> 1. copy Martinos Center dicoms to my local Mac
> 2. import dicoms into OsiriX
> 3. Export them as dicoms
> 4. copy the OsiriX-exported dicoms back to Launchpad
> 5. Run dcm2niix on the new dicoms
>
> Since this copying back and forth takes a lot of time, I need a better
> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones!
>
> I would really appreciate your help.
>
> Best,
> Emad
>
>
> Emad Ahmadi, MD
> ---
> Research Fellow
> Department of Radiology
> Massachusetts General Hospital
> Harvard Medical School
>
> 25 New Chardon Street, Suite 400
> Boston, MA 02114
> Tel: 617 726 5237
> Email: e...@nmr.mgh.harvard.edu 
>
>
>
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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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[Freesurfer] Voxel based vs surface based

2015-10-30 Thread John Anderson

Hi Doug and Bruce,
Kindly, I have question regarding the difference between voxel based ( VBM/ FSL pipeline) and surface based analysis ( Freesurfer ).
 
I have two groups of subjects Group A and Group B
I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to check the difference in cortical thickness between the groups. Then I used Qdec to correct the results for multiple comparisons and to visualize the significant clusters.
Then I ran VBM analysis between the groups ( the same subjects) to study the difference in gray matter volume between the groups.
 
I got significant difference between the groups in both methods but in different areas of the brain ( the significant clusters are not in the same location ).
 
What is the difference between surface based analysis and voxel based analysis technically. Is it right to get different results?
 
Thanks in advance

 

 

 

Bests,
John 

 
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Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

2015-10-30 Thread Douglas Greve

you can also try mri_convert from the dev env.  It should recognize the 
diffusion scan and write out the bval/bvecs

On 10/30/15 10:43 AM, dgw wrote:
> Hi Emad,
>
> The only problems, which I have run into is major weaknesses in dcm2nii:
> 1. You must have write permissions on the directory the files are
> located in.
> 2. dcm2nii cannot work on symbolically linked files.
>
> Therefore, first copy the files to your own analysis workspace: e.g.
> /cluster//
> then run dcm2nii.
> With that I have no problems.
>
> hth
> d
>
> On 10/30/15 10:28 AM, Emad Ahmadi wrote:
>> Hi Freesurfer experts,
>>
>> I hope you’re all enjoying your day!
>>
>> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms
>> obtained at Martinos Center. The dicoms have the following format:
>>
>> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919
>> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196
>> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464
>> ...
>>
>> I receive error when I run dcm2niix (to extract the b values and b
>> vectors):
>>
>> Command:
>> dcm2niix -f dti 
>>
>> The error I receive:
>>
>> Warning: output folder invalid
>> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try
>> Error: unable to find any DICOM images in
>> Conversion required 0.00 seconds.
>>
>> When I do the following steps to generate “treatable” dicoms, dcm2niix
>> recognizes these dicoms:
>>
>> 1. copy Martinos Center dicoms to my local Mac
>> 2. import dicoms into OsiriX
>> 3. Export them as dicoms
>> 4. copy the OsiriX-exported dicoms back to Launchpad
>> 5. Run dcm2niix on the new dicoms
>>
>> Since this copying back and forth takes a lot of time, I need a better
>> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones!
>>
>> I would really appreciate your help.
>>
>> Best,
>> Emad
>>
>>
>> Emad Ahmadi, MD
>> ---
>> Research Fellow
>> Department of Radiology
>> Massachusetts General Hospital
>> Harvard Medical School
>>
>> 25 New Chardon Street, Suite 400
>> Boston, MA 02114
>> Tel: 617 726 5237
>> Email: e...@nmr.mgh.harvard.edu 
>>
>>
>>
>> ___
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Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

2015-10-30 Thread Emad Ahmadi

Hi,

Thank you for your quick response!

I have already copied the dicoms to my cluster space:

/cluster/guptagp/Emad/Epilepsy/temp/slices

and the permissions of this folder seem right to me:

drwxrwsr-x 2 emad guptagp 32768 Oct 30 10:30 slices

The permissions on the dicom files are the same:

-bash-4.1$ ls -l MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700

-rwxrwxr-x 1 emad guptagp 2219694 Oct 30 10:30 
MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700


Any thoughts?

Best,
Emad



> On Oct 30, 2015, at 10:43 AM, dgw  wrote:
> 
> Hi Emad,
> 
> The only problems, which I have run into is major weaknesses in dcm2nii:
> 1. You must have write permissions on the directory the files are 
> located in.
> 2. dcm2nii cannot work on symbolically linked files.
> 
> Therefore, first copy the files to your own analysis workspace: e.g. 
> /cluster//
> then run dcm2nii.
> With that I have no problems.
> 
> hth
> d
> 
> On 10/30/15 10:28 AM, Emad Ahmadi wrote:
>> Hi Freesurfer experts,
>> 
>> I hope you’re all enjoying your day!
>> 
>> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms
>> obtained at Martinos Center. The dicoms have the following format:
>> 
>> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919
>> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196
>> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464
>> ...
>> 
>> I receive error when I run dcm2niix (to extract the b values and b
>> vectors):
>> 
>> Command:
>> dcm2niix -f dti 
>> 
>> The error I receive:
>> 
>> Warning: output folder invalid
>> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try
>> Error: unable to find any DICOM images in
>> Conversion required 0.00 seconds.
>> 
>> When I do the following steps to generate “treatable” dicoms, dcm2niix
>> recognizes these dicoms:
>> 
>> 1. copy Martinos Center dicoms to my local Mac
>> 2. import dicoms into OsiriX
>> 3. Export them as dicoms
>> 4. copy the OsiriX-exported dicoms back to Launchpad
>> 5. Run dcm2niix on the new dicoms
>> 
>> Since this copying back and forth takes a lot of time, I need a better
>> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones!
>> 
>> I would really appreciate your help.
>> 
>> Best,
>> Emad
>> 
>> 
>> Emad Ahmadi, MD
>> ---
>> Research Fellow
>> Department of Radiology
>> Massachusetts General Hospital
>> Harvard Medical School
>> 
>> 25 New Chardon Street, Suite 400
>> Boston, MA 02114
>> Tel: 617 726 5237
>> Email: e...@nmr.mgh.harvard.edu  
>> >

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Re: [Freesurfer] error vcsf.config

2015-10-30 Thread Douglas Greve

That means it could not find any CSF voxels. Try checking the 
registration. It could also be that this is a subject with really small 
ventricles.


On 10/30/15 3:57 AM, std...@virgilio.it wrote:


Hi list,


During fcseed-sess -s subj -cfg vcsf.config


a subject produces the follow error.

I have rerun recon-all, cheched aparc+aseg with tkmedit. They seem to 
be ok.


Why this error is produced?


Thanks



Stefano



Creating output directory 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm


Loading y from 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz


Saving design matrix to 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat


Normalized matrix condition is 61.5872

Matrix condition is 1e+08

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to 
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh


search space = 0.00

DOF = 297

Starting fit and test

Fit completed in 0.0008 minutes

Computing temporal AR1

Writing results

Computing FSNR

  mean

maxvox sig=0  F=0  at  index 0 0 0 seed=1446518089

  linear

maxvox sig=0  F=0  at  index 0 0 0 seed=1446518089

  quad

maxvox sig=0  F=0  at  index 0 0 0 seed=1446518089

Computing PCA (300)

ERROR: no voxels in mask



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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

2015-10-30 Thread Douglas Greve

You can also load the new segmentation into freeview and see the 
segmentation number that each gets. If you can get the color table out 
of the annotation, then the segmentation number will be 1000+ that 
number (left hemi) and 2000+that number for the right

On 10/30/15 8:30 AM, Bruce Fischl wrote:
> what is the laus250 parcellation? The lookup tables are in text so you
> should be able to open one in an editor and see what the format is. It's
> pretty straightforward. # lines are comments, then it is
>
>  
>
> cheers
> Bruce
>
>
> On Fri, 30 Oct 2015, Peled, Noam wrote:
>
>> Hey all,
>> I used mri_aparc2aseg to map the cortical labels from the laus250 
>> parcellation.
>> Now I need to create a new lookup table, mainly for displaying the labels' 
>> names in freeview.
>> How can I know what id each label gets in my new laus+aseg.mgz file?
>>
>> Thanks,
>> Noam
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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

2015-10-30 Thread Peled, Noam

Hey Bruce,
I meant for the Lausanne250 parcellation 
(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048121)
The problem is with the #index column. To create a custom lookup table, I need 
to know what is the #index each label gets in the output file of
mri_aparc2aseg.
I want to users to be able to load this new mgz file into freeview with the 
right lookup table.

Thanks,
Noam

On Fri, 30 Oct 2015, Bruce wrote:

> what is the laus250 parcellation? The lookup tables are in text so you
> should be able to open one in an editor and see what the format is. It's
> pretty straightforward. # lines are comments, then it is

>  

> cheers
> Bruce

On Fri, 30 Oct 2015, Peled, Noam wrote:

> Hey all,
> I used mri_aparc2aseg to map the cortical labels from the laus250
> parcellation.
> Now I need to create a new lookup table, mainly for displaying the labels'
> names in freeview.
> How can I know what id each label gets in my new laus+aseg.mgz file?
>
> Thanks,
> Noam
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Re: [Freesurfer] average z-score of each subject from a common cluster

2015-10-30 Thread Douglas Greve




On 10/30/15 7:16 AM, std...@virgilio.it wrote:

Hi list,
I have two queries, please.

I'd like to have the z-score from my rsfMRI data (seed-analyis).

1) I have extract the z-score from the Vtx Max

In details, after groups comparison analysis, I have opened 
the cache.th13.pos.sig.cluster.summary contained in group.diff folder 
and I have read the Vtx Max coordinates.
Next, I have open the z.nii.gz of each subject and I have expected the 
z-score from the vertex which have the Vtx Max coordinates.


Is this procedure corrected?

Yes


2) z-score of each subject from a common cluster

I would like to use the cluster which shows the group difference 
(cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract 
from it the average of the z-score which is contained in each subject.

How should I do?
Use mri_segstats passing the z map as the input (--i) and the cluster 
map as the seg. The output will be --sum. Run with --help for more info


Thanks.


Stefano



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Re: [Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

2015-10-30 Thread Knut Jørgen Bjuland

Hi

I have disable System_Integrity_Protection to get free surfer working on El 
Capitan


Knut Jorgen


On 30 Oct 2015, at 15:16, Z K  wrote:
> 
> There are significant changes in the most recent OSX release El Capitan 
> and this is one consequence of them 
> (https://en.wikipedia.org/wiki/OS_X_El_Capitan#System_Integrity_Protection). 
> We are currently exploring solutions but as of right now, freesurfer is 
> not fully functional on OS X 10.11
> 
> 
> 
> On 10/30/2015 04:45 AM, Knut Jørgen Bjuland wrote:
>> 
>> Hi
>> 
>> 
>> When I start freeview form command line on Mac OS X 11.10 it crash with
>> this error message. Do I miss a file?
>> 
>> 
>> 
>> freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated
>> 
>> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>> 
>>   Referenced from:
>> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>> 
>>   Expected in: /usr/lib/libSystem.B.dylib
>> 
>> 
>> dyld: Symbol not found: ___emutls_get_address
>> 
>>   Referenced from:
>> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>> 
>>   Expected in: /usr/lib/libSystem.B.dylib
>> 
>> 
>> [0]PETSC ERROR:
>> 
>> 
>> [0]PETSC ERROR: Caught signal number 5 TRAP
>> 
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> 
>> [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
>> find memory corruption errors
>> 
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> 
>> [0]PETSC ERROR: to get more information on the crash.
>> 
>> [0]PETSC ERROR: - Error Message
>> 
>> 
>> [0]PETSC ERROR: Signal received!
>> 
>> [0]PETSC ERROR:
>> 
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> 
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> 
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> 
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> 
>> [0]PETSC ERROR:
>> 
>> 
>> [0]PETSC ERROR: Unknown Name on a darwin12. named
>> Knuts-MacBook-Pro.local by knutjorgenbjulan Fri Oct 30 09:42:53 2015
>> 
>> [0]PETSC ERROR: Libraries linked from
>> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
>> 
>> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
>> 
>> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
>> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
>> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> 
>> [0]PETSC ERROR:
>> 
>> 
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> 
>> [unset]: aborting job:
>> 
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> 
>> 
>> Knut Jørgen Bjuland
>> NTNU
>> 
>> 
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Re: [Freesurfer] unit in 'search area' in the glmfit log

2015-10-30 Thread Douglas Greve

That number is in voxels or vertices. If you want surface area, then use 
mri_segstats something like

mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh 
--seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat

doug

On 10/29/15 5:10 PM, Jeni Chen wrote:
> Hello,
>
> When running the Clusterwise Correction for Multiple Comparisons, I used a 
> label as a mask to restrict search area. I want to find out the size of that 
> label, so I guess I can pull that information out from the "mri_glmfit.log", 
> specifically under 'searchspace'? Also I only see a numerical value there, I 
> assume it is in mm2?
>
> Thanks.
>
> Jeni
>
>
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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

2015-10-30 Thread Bruce Fischl

Hi Noam

we should just preserve whatever index they use

cheers
Bruce
On Fri, 30 Oct 2015, Peled, 
Noam wrote:

> 
> Hey Bruce,
> I meant for the Lausanne250 parcellation (http://journals.plos.org/plosone/a
> rticle?id=10.1371/journal.pone.0048121)
> The problem is with the #index column. To create a custom lookup table, I ne
> ed to know what is the #index each label gets in the output file of 
> mri_aparc2aseg.
> I want to users to be able to load this new mgz file into freeview with the 
> right lookup table.
> Thanks,
> Noam
> On Fri, 30 Oct 2015, Bruce wrote:
> > what is the laus250 parcellation? The lookup tables are in text so you 
> > should be able to open one in an editor and see what the format is. It's 
> > pretty straightforward. # lines are comments, then it is
> 
> >  
> 
> > cheers
> > Bruce
> 
> 
> On Fri, 30 Oct 2015, Peled, Noam wrote:
> 
> > Hey all,
> > I used mri_aparc2aseg to map the cortical labels from the laus250 
> > parcellation.
> > Now I need to create a new lookup table, mainly for displaying the labels'
> 
> > names in freeview.
> > How can I know what id each label gets in my new laus+aseg.mgz file?
> >
> > Thanks,
> > Noam
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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Re: [Freesurfer] wrong segmentation

2015-10-30 Thread Bruce Fischl

what version are you using? I think this won't happen in V6,but if you 
upload the subject dir I can check for you. To fix it check and correct 
the wm.mgz and the aseg.mgz in that region


cheers
Bruce
On Thu, 29 Oct 2015, Thục Trinh 
wrote:



Hi Freesurfer experts,
I ran recon-all for our subjects and there is a problem with the wrong
segmentation between the white/gray matter. this error appears in couples
continued slices. Picture are attached.
Do you have any suggestion to fix this error. 

Thank you,
Trinh

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Re: [Freesurfer] Voxel based vs surface based

2015-10-30 Thread Bruce Fischl


Hi John

yes, they are different methods that measure somewhat different things so 
there is no reason they would show the same maps. If you look at volume 
change in FS it might be closer, but even that won't match VBM 
necessarily


cheers
Bruce
On Fri, 30 Oct 2015, John Anderson wrote:


Hi Doug and Bruce,
Kindly, I have question regarding the difference between voxel based ( VBM/
FSL pipeline) and surface based analysis ( Freesurfer ).
 
I have two groups of subjects Group A and Group B
I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to
check the difference in cortical thickness between the groups. Then I used
Qdec to correct the results for multiple comparisons and to visualize the
significant clusters.
Then I ran VBM analysis between the groups ( the same subjects) to study the
difference in gray matter volume between the groups.
 
I got significant difference between the groups in both methods but in
different areas of the brain ( the significant clusters are not in the same
location ).
 
What is the difference between surface based analysis and voxel based
analysis technically. Is it right to get different results?
 
Thanks in advance
 
 
 
Bests,
John 

 

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[Freesurfer] Free surfer dev env doesn't extract bvals/bvecs

2015-10-30 Thread Emad Ahmadi

Hi Freesurfers,I’m using the dev env on Launchpad to analyze DTI dicoms using TRACULA.It cannot extract the bvecs from the dicom header since it gives me the following error:ERROR: Must specify input table of gradient vectorsI’ve attached the TRACULA configuration file (dmrirc3.txt) and the log file. I would appreciate your help!Best,Emad
Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#_
setenv SUBJECTS_DIR /cluster/guptagp/Emad/Epilepsy/subjDir
setenv RAW_DATA /cluster/guptagp/Emad/Epilepsy/rawData
#_

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
#set dtroot = /path/to/tracts/of/ducks

# Subject IDs
#_
set subjlist = (310)
#_

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 3)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified (see below)
#_
set dcmroot = $RAW_DATA
set dcmlist = 
(310/DIFFUSION_high_res/slices/MR1.3.12.2.1107.5.2.32.35006.2009020220092419345382942)
#_

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
#set bveclist = ()

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
#set bvecfile = /path/to/bvecs.txt

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
#set bvalfile = /path/to/bvals.txt

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
#set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm 
louie/fphas/XXX-1.dcm)

# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
#set echospacing = 0.7

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
#
#set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
#
#set dorotbvecs = 1

# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
#set thrbet = 0.5

# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
#
set doregflt = 1

# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 0

# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
#set doregmni = 1

# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
#set mnitemp = /path/to/mni_template.nii.gz

# Perform registration of T1 to CVS template?
# Default: 0 (no)
#
#set doregcvs = 0

# CVS template subject ID
# Only used if doregcvs = 1
# Default: cvs_avg35
#
#set cvstemp = donald

# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
#
#set cvstempdir = /path/to/cvs/atlases/of/ducks

# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
#set usemaskanat = 1

# Paths to reconstruct
# Default: All paths in the atlas
#
#set pathlist = ( lh.cst_AS rh.cst_AS \
 lh.unc_AS rh.unc_AS \
 lh.ilf_AS rh.ilf_AS \
 fmajor_PP fminor_PP \
 lh.atr_PP rh.atr_PP \
 lh.ccg_PP rh.ccg_PP \
 lh.cab_PP rh.cab_PP \

Re: [Freesurfer] Voxel based vs surface based

2015-10-30 Thread O'Shea,Andrew

Hello John,
I would highly recommend you take a look at this paper 
http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf (Greve, 
2011. An Absolute Beginner's Guide to Surface- and Voxel-
based Morphometric Analysis). I have found it to be very helpful for my 
understanding.
-Andrew

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of John Anderson 
mailto:j.ander...@publicist.com>>
Reply-To: 
"freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 30, 2015 at 10:54 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Voxel based vs surface based

Hi Doug and Bruce,
Kindly, I have question regarding the difference between voxel based ( VBM/ FSL 
pipeline) and surface based analysis ( Freesurfer ).

I have two groups of subjects Group A and Group B
I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to 
check the difference in cortical thickness between the groups. Then I used Qdec 
to correct the results for multiple comparisons and to visualize the 
significant clusters.
Then I ran VBM analysis between the groups ( the same subjects) to study the 
difference in gray matter volume between the groups.

I got significant difference between the groups in both methods but in 
different areas of the brain ( the significant clusters are not in the same 
location ).

What is the difference between surface based analysis and voxel based analysis 
technically. Is it right to get different results?

Thanks in advance



Bests,
John


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[Freesurfer] changing the index of labels

2015-10-30 Thread Jacobs H (NP)


Hi,

Is there a way to change the index of the segmentation of the hippocampal
subfields, so that when I combine left and right, FreeSurfer treats them
as different regions?

Thanks!
Best
Heidi

>
>>I just checked again in freeview and indeed they have the same index
>>(e.g.
>>CA1 has value 206 for left and also for right).
>>
>>On 10/27/15, 5:01 PM, "Douglas Greve"  wrote:
>>
>>>The color is not important. The question is whether they have a
>>>different index. Can you confirm that lh and rh have the same index?
>>>
>>>On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
 Hi Doug,

 Yes, for the aseg they are. But not for the hippocampal subfields:
left
 and right have the same color coding.
 I am creating one segmentation, including left and right hippocampal
 subfields and aparc, for partial volume correction.
 Any idea how I can make the labels for the hippocampal subfields
different
 (freesurfer version 6)?

 Thanks
 Heidi

 On 10/27/15, 4:32 PM, "Douglas Greve" 
wrote:

> The indices should be different. Eg, 17 is left hippo, 53 is right
> hippo. If you click on them in freeview and different labels appear,
> then FS knows they are different
>
> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>> Hi.
>>
>> Just one another related question: now that I was able to combine
>>left
>> and
>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>> that
>> the left and right hippocampal subfields have the same color labels
>>and
>> codes. What would be the best way to make sure that FreeSurfer
>> understand
>> that the left and right subfields (e.g. Left and right CA1) are
>> different
>> areas? 
>>
>> Thanks!
>> Heidi
>>
>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>> 
>> wrote:
>>
>>> Thanks! Works wonderful!
>>> Heidi
>>>
>>> On 10/21/15, 10:50 PM, "Douglas N Greve"
>>>
>>> wrote:
>>>
 If you want to remove them, you can use mri_binarize with the
 --replace
 option, replacing them with whatever you want.

 On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
> Hi,
>
> I am trying to generate a segmentation file containing the
>aseg+aparc
> but replacing the hippocampus with the hippocampal subfields.
> With mergeseg I was able to merge the segmentations, but
> unfortunately
> parts of the ³old² hippocampus (labeled as 17 and 53) are still
>in
> there (as the area covered by the subfields is not 100% equal to
>the
> hippocampus of the aseg).
> How can I remove the remains of the old hippocampal labels?
>
> Many thanks!
> Best
> Heidi
>
>
> ___
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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
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 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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 is
 addressed. If you believe this e-mail was sent to you in error and
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 e-mail
 contains patient information, please contact the Partners
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 you in
 error
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>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>>>
>>>___
>>>Freesurfer mai

Re: [Freesurfer] changing the index of labels

2015-10-30 Thread Bruce Fischl


Hi Heidi

I guess you could do it yourself in matlab using the aseg to figure out 
which hemisphere you are in


cheers
Bruce

On Fri, 30 Oct 2015, Jacobs H (NP) wrote:



Hi,

Is there a way to change the index of the segmentation of the hippocampal
subfields, so that when I combine left and right, FreeSurfer treats them
as different regions?

Thanks!
Best
Heidi




I just checked again in freeview and indeed they have the same index
(e.g.
CA1 has value 206 for left and also for right).

On 10/27/15, 5:01 PM, "Douglas Greve"  wrote:


The color is not important. The question is whether they have a
different index. Can you confirm that lh and rh have the same index?

On 10/27/15 11:53 AM, Jacobs H (NP) wrote:

Hi Doug,

Yes, for the aseg they are. But not for the hippocampal subfields:
left
and right have the same color coding.
I am creating one segmentation, including left and right hippocampal
subfields and aparc, for partial volume correction.
Any idea how I can make the labels for the hippocampal subfields
different
(freesurfer version 6)?

Thanks
Heidi

On 10/27/15, 4:32 PM, "Douglas Greve" 
wrote:


The indices should be different. Eg, 17 is left hippo, 53 is right
hippo. If you click on them in freeview and different labels appear,
then FS knows they are different

On 10/24/15 9:29 PM, Jacobs H (NP) wrote:

Hi.

Just one another related question: now that I was able to combine
left
and
right hippocampal subfields with the aparc-aseg correctly, I noticed
that
the left and right hippocampal subfields have the same color labels
and
codes. What would be the best way to make sure that FreeSurfer
understand
that the left and right subfields (e.g. Left and right CA1) are
different
areas?

Thanks!
Heidi

On 10/21/15, 11:01 PM, "Jacobs H (NP)"

wrote:


Thanks! Works wonderful!
Heidi

On 10/21/15, 10:50 PM, "Douglas N Greve"

wrote:


If you want to remove them, you can use mri_binarize with the
--replace
option, replacing them with whatever you want.

On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:

Hi,

I am trying to generate a segmentation file containing the
aseg+aparc
but replacing the hippocampus with the hippocampal subfields.
With mergeseg I was able to merge the segmentations, but
unfortunately
parts of the ³old² hippocampus (labeled as 17 and 53) are still
in
there (as the area covered by the subfields is not 100% equal to
the
hippocampus of the aseg).
How can I remove the remains of the old hippocampal labels?

Many thanks!
Best
Heidi


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--
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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] cortical thickness - comparing two groups within a ROI

2015-10-30 Thread Eryilmaz, H. Hamdi

Dear FS experts,

I have a question about extracting average cortical thickness from a manually 
created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd 
file appears as the following:

GroupDescriptorFile 1
Title PostPreFortification
Class PostFort
Class PreFort

InputSubject1PostFort
InputSubject2PostFort
.
.
.

The contrast that I use to compare these groups is [1 -1]. When I display the 
significance map for this contrast I get the following image on the left 
hemisphere:

[X]


My first question is, those blue clusters represent regions, where thickness is 
greater in the PreFort group, don't they? Assuming this is correct, I created a 
label for this region (which contains about 3000 vertices) and extracted the 
thickness value from this region for each subject using the following commands. 
These commands are part of scripts in which $subject and $label are defined.

[X]

to make a label for each subject (the original label was created on fsaverage):
mri_label2label --srclabel $SUBJECTS_DIR/labels/${label}.label --srcsubject 
fsaverage --trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject 
$subject --regmethod surface --hemi lh

to create a stats file of this ROI containing several anatomical measures:
mris_anatomical_stats -f 
$SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l 
$SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh

to compile thickness values from all subjects into one table:
aparcstats2table --hemi lh --subjectsfile 
$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc 
NP_PostMINUSPre_IPS.label --meas thickness --tablefile 
$SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt

This table displays the average thickness value of my ROI for each subject. 
Based on this table I calculated the mean thickness for each group, which is as 
the following:

PostFort: 3.043
PreFort: 2.842

My question is: If this cluster appears blue in the Post>Pre map, shouldn't the 
thickness have been greater in the PreFort group? Or am I missing a step?

Many thanks in advance!

Best,
Hamdi

















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[Freesurfer] R: Re: error vcsf.config

2015-10-30 Thread stdp82

Yes, the ventricle is very small.
The segmentation in aparc and aseg is nice.How can I do to analyze this 
subject? I need to include it in the analysis.Many thanks,

Stefano




Messaggio originale

Da: gr...@nmr.mgh.harvard.edu

Data: 30-ott-2015 16.03

A: 

Ogg: Re: [Freesurfer] error vcsf.config




  
  
That means it could not find any CSF voxels. Try checking the
registration. It could also be that this is a subject with really
small ventricles.



On 10/30/15 3:57 AM, std...@virgilio.it
  wrote:



  Hi list,
  

  
  During fcseed-sess -s subj -cfg vcsf.config
  

  
  a subject produces the follow error.
  I have rerun recon-all, cheched aparc+aseg
with tkmedit. They seem to be ok.
  Why this error is produced?
  

  
  Thanks
  

  
  

  
  Stefano
  

  
  

  
  Creating output directory
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm
  Loading y from
/Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz
  Saving design matrix to
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat
  Normalized matrix condition is 61.5872
  Matrix condition is 1e+08
  Pruning voxels by thr: 0.00
  Found 0 voxels in mask
  Saving mask to
/Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh
  search space = 0.00
  DOF = 297
  Starting fit and test
  Fit completed in 0.0008 minutes
  Computing temporal AR1
  Writing results
  Computing FSNR
mean
  maxvox sig=0  F=0  at  index 0 0 0   
seed=1446518089
linear
  maxvox sig=0  F=0  at  index 0 0 0   
seed=1446518089
quad
  maxvox sig=0  F=0  at  index 0 0 0   
seed=1446518089
  Computing PCA (300)
  ERROR: no voxels in mask
  

  
  

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[Freesurfer] TRACULA question- pathstats not loading

2015-10-30 Thread Golan, Noa

Hi, 
I am currently analyzing DTI data and I am having issues with one file in 
particular. When I run the tracheal -path -c step, all of the files are 
generated except the pathstats text files. 

Any thoughts?

Thanks!
Noa
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Re: [Freesurfer] bring volumes to fsaverage space

2015-10-30 Thread Shani Ben Amitay

Hello
Can you please direct me to more information about the CVS.
Thanks!
Shani
בתאריך 30 באוק' 2015 14:39,‏ "Bruce Fischl" 
כתב:

> Hi Shani
>
> you can use mri_vol2vol with the talairach.m3z. Alternatively, you can run
> CVS which will give you more accurate cortical matching and use the
> transform that it produces.
>
> cheers
> Bruce
> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>
> Dear freesurfers,
>> I would like to know what will be the best way to bring volumes in the
>> individual subject's space  to the fsaverage space.
>>
>> Thanks,
>> Shani
>>
>>
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[Freesurfer] R: Re: average z-score of each subject from a common cluster

2015-10-30 Thread stdp82

Thanks.I have obtained:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i z.nii.gz 
--sum summaryfile 
sysname  Darwin
hostname iMac-di-Stefano.local
machine  x86_64
user Stefano
UseRobust  0
Loading z.nii.gz
Loading z.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  22 segmentations
Computing statistics for each segmentation
  0-7  2   2.000
  1-6110 110.000
  2-5255 255.000
  3-4518 518.000
  4-3   11901190.000
  5-2   16921692.000
  6-1   41044104.000
  7 0  61577   61577.000
  8 1  42598   42598.000
  9 2  28146   28146.000
 10 3  14859   14859.000
 11 4   58455845.000
 12 5   18991899.000
 13 6485 485.000
 14 7116 116.000
 15 8 75  75.000
 16 9 74  74.000
 1710 78  78.000
 1811 65  65.000
 1912104 104.000
 2013 45  45.000
 2114  5   5.000
How I can know the meaning of this number? Where is z? I have tried also 
with:mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii.gz --sum 
summaryfile --mask 
.../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13.neg.sig.masked.nii.gz
 --avgwfvol mrivol
but I have problem with interpretation.

Stefano



Messaggio originale

Da: gr...@nmr.mgh.harvard.edu

Data: 30-ott-2015 16.17

A: 

Ogg: Re: [Freesurfer] average z-score of each subject from a common cluster




  
  




On 10/30/15 7:16 AM, std...@virgilio.it
  wrote:


Hi list,
  I have two queries, please.
  

  
  I'd like to have the z-score from my rsfMRI data
(seed-analyis).
  

  
  1) I have extract the z-score from the Vtx Max
  

  
  In details, after groups comparison analysis, I have opened
the cache.th13.pos.sig.cluster.summary contained in group.diff
folder and I have read the Vtx Max coordinates.
  Next, I have open the z.nii.gz of each subject and I have
expected the z-score from the vertex which have the Vtx Max
coordinates.
  

  
  Is this procedure corrected?

Yes


  

  
  2) z-score of each subject from a common cluster
  

  
  I would like to use the cluster which shows the group
difference (cache.th13.pos.sig.cluster.nii.gz) as ROI mask.
Thus, I would extract from it the average of the z-score which
is contained in each subject.
  How should I do? 

  

Use mri_segstats passing the z map as the input (--i) and the
cluster map as the seg. The output will be --sum. Run with --help
for more info


  

  
  Thanks.
  

  
  

  
  Stefano
  

  
  

  
  

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[Freesurfer] Fwd: 2015 Call for Communications Committee Members

2015-10-30 Thread Douglas N Greve

 Forwarded Message 
Subject:2015 Call for Communications Committee Members
Date:   Fri, 30 Oct 2015 11:34:52 -0500
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu

Dear OHBM Members:

The Organization for Human Brain Mapping is pleased to announce the 
formation of a Communications Committee. The Council elected Randy 
Gollub as Chair and Nikolaus Kriegeskorte as Chair Elect of 
the Communications Committee. The formation of this Committee was 
approved by the OHBM Council at it's recent strategic planning meeting. 
The primary goal of this Committee is to increase the visibility and 
impact of members' work within the OHBM community and to extend it to a 
broader audience. The Communications Committee is now seeking volunteers 
from a variety of interest areas, geographic locations and experience 
levels, to serve on this Committee for a three year term.

The Communication Committee will be comprised of twelve to fifteen 
current OHBM members with interest and experience in writing, editing, 
social media, media relations or communications. We are seeking 
candidates with skills in these areas to support communication efforts 
for different audiences, content areas and functions.

We welcome you to participate in this very important new OHBM 
initiative. If interested, please complete the Call for Volunteers 
online form  no later 
than Monday, November 16.  To apply you must be current member of OHBM 
(Renew membership now at www.humanbrainmapping.org 
). Submitted applications will be 
presented to the Communications Committee Chair, Randy Gollub, and 
Co-Chair Niko Kriegeskorte for consideration and selection.

If you have any questions, please contact OHBM at 
i...@humanbrainmapping.org .

Sincerely,

Karl Zilles, Chair
Organization for Human Brain Mapping

Randy Gollub, Chair
OHBM Communications Committee

Niko Kriegeskorte, Chair-Elect
OHBM Communications Committee

*Organization for Human Brain Mapping*
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
Phone: 1 952-646-2029
Fax: 1 952-545-6073
www.humanbrainmapping.org 
i...@humanbrainmapping.org 

To opt out of OHBM emails, contact the OHBM Executive Office at 
i...@humanbrainmapping.org 
.

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

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Re: [Freesurfer] bring volumes to fsaverage space

2015-10-30 Thread Lilla Zollei



Hi Shani,

Sure. You can do

mri_cvs_register --help

and that should give you lots of information.

Alternatively you can also go to 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register


and read through the presentation that we give at the FS course:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt

Best, Lilla

On Fri, 30 Oct 2015, Shani Ben Amitay wrote:



Hello
Can you please direct me to more information about the CVS.
Thanks!
Shani

בתאריך 30 באוק' 2015 14:39, "Bruce Fischl"  כתב:
  Hi Shani

  you can use mri_vol2vol with the talairach.m3z. Alternatively, you can 
run CVS which will give you more accurate cortical matching and use the 
transform that it produces.

  cheers
  Bruce
  On Fri, 30 Oct 2015, Shani Ben Amitay wrote:

Dear freesurfers,
I would like to know what will be the best way to bring volumes in 
the
individual subject's space  to the fsaverage space.

Thanks, 
Shani


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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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Re: [Freesurfer] changing the index of labels

2015-10-30 Thread Douglas N Greve


Are there different files for the lh and rh? Sorry, never done the 
subfields analysis.


On 10/30/2015 01:25 PM, Bruce Fischl wrote:
> Hi Heidi
>
> I guess you could do it yourself in matlab using the aseg to figure 
> out which hemisphere you are in
>
> cheers
> Bruce
>
> On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
>
>>
>> Hi,
>>
>> Is there a way to change the index of the segmentation of the 
>> hippocampal
>> subfields, so that when I combine left and right, FreeSurfer treats them
>> as different regions?
>>
>> Thanks!
>> Best
>> Heidi
>>
>>>
 I just checked again in freeview and indeed they have the same index
 (e.g.
 CA1 has value 206 for left and also for right).

 On 10/27/15, 5:01 PM, "Douglas Greve"  
 wrote:

> The color is not important. The question is whether they have a
> different index. Can you confirm that lh and rh have the same index?
>
> On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>> Hi Doug,
>>
>> Yes, for the aseg they are. But not for the hippocampal subfields:
>> left
>> and right have the same color coding.
>> I am creating one segmentation, including left and right hippocampal
>> subfields and aparc, for partial volume correction.
>> Any idea how I can make the labels for the hippocampal subfields
>> different
>> (freesurfer version 6)?
>>
>> Thanks
>> Heidi
>>
>> On 10/27/15, 4:32 PM, "Douglas Greve" 
>> wrote:
>>
>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>> hippo. If you click on them in freeview and different labels 
>>> appear,
>>> then FS knows they are different
>>>
>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
 Hi.

 Just one another related question: now that I was able to combine
 left
 and
 right hippocampal subfields with the aparc-aseg correctly, I 
 noticed
 that
 the left and right hippocampal subfields have the same color 
 labels
 and
 codes. What would be the best way to make sure that FreeSurfer
 understand
 that the left and right subfields (e.g. Left and right CA1) are
 different
 areas?

 Thanks!
 Heidi

 On 10/21/15, 11:01 PM, "Jacobs H (NP)"
 
 wrote:

> Thanks! Works wonderful!
> Heidi
>
> On 10/21/15, 10:50 PM, "Douglas N Greve"
> 
> wrote:
>
>> If you want to remove them, you can use mri_binarize with the
>> --replace
>> option, replacing them with whatever you want.
>>
>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>> Hi,
>>>
>>> I am trying to generate a segmentation file containing the
>>> aseg+aparc
>>> but replacing the hippocampus with the hippocampal subfields.
>>> With mergeseg I was able to merge the segmentations, but
>>> unfortunately
>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still
>>> in
>>> there (as the area covered by the subfields is not 100% 
>>> equal to
>>> the
>>> hippocampus of the aseg).
>>> How can I remove the remains of the old hippocampal labels?
>>>
>>> Many thanks!
>>> Best
>>> Heidi
>>>
>>>
>>> ___
>>> 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
>>

Re: [Freesurfer] changing the index of labels

2015-10-30 Thread Jacobs H (NP)

Yes, there are different mgz files for left and right (but they have the
same index numbers and colors).

On 10/30/15, 11:16 PM, "Douglas N Greve"  wrote:

>
>Are there different files for the lh and rh? Sorry, never done the
>subfields analysis.
>
>
>On 10/30/2015 01:25 PM, Bruce Fischl wrote:
>> Hi Heidi
>>
>> I guess you could do it yourself in matlab using the aseg to figure
>> out which hemisphere you are in
>>
>> cheers
>> Bruce
>>
>> On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
>>
>>>
>>> Hi,
>>>
>>> Is there a way to change the index of the segmentation of the
>>> hippocampal
>>> subfields, so that when I combine left and right, FreeSurfer treats
>>>them
>>> as different regions?
>>>
>>> Thanks!
>>> Best
>>> Heidi
>>>

> I just checked again in freeview and indeed they have the same index
> (e.g.
> CA1 has value 206 for left and also for right).
>
> On 10/27/15, 5:01 PM, "Douglas Greve" 
> wrote:
>
>> The color is not important. The question is whether they have a
>> different index. Can you confirm that lh and rh have the same index?
>>
>> On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>>> Hi Doug,
>>>
>>> Yes, for the aseg they are. But not for the hippocampal subfields:
>>> left
>>> and right have the same color coding.
>>> I am creating one segmentation, including left and right
>>>hippocampal
>>> subfields and aparc, for partial volume correction.
>>> Any idea how I can make the labels for the hippocampal subfields
>>> different
>>> (freesurfer version 6)?
>>>
>>> Thanks
>>> Heidi
>>>
>>> On 10/27/15, 4:32 PM, "Douglas Greve" 
>>> wrote:
>>>
 The indices should be different. Eg, 17 is left hippo, 53 is right
 hippo. If you click on them in freeview and different labels
 appear,
 then FS knows they are different

 On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
> Hi.
>
> Just one another related question: now that I was able to combine
> left
> and
> right hippocampal subfields with the aparc-aseg correctly, I
> noticed
> that
> the left and right hippocampal subfields have the same color
> labels
> and
> codes. What would be the best way to make sure that FreeSurfer
> understand
> that the left and right subfields (e.g. Left and right CA1) are
> different
> areas?
>
> Thanks!
> Heidi
>
> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
> 
> wrote:
>
>> Thanks! Works wonderful!
>> Heidi
>>
>> On 10/21/15, 10:50 PM, "Douglas N Greve"
>> 
>> wrote:
>>
>>> If you want to remove them, you can use mri_binarize with the
>>> --replace
>>> option, replacing them with whatever you want.
>>>
>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
 Hi,

 I am trying to generate a segmentation file containing the
 aseg+aparc
 but replacing the hippocampus with the hippocampal subfields.
 With mergeseg I was able to merge the segmentations, but
 unfortunately
 parts of the ³old² hippocampus (labeled as 17 and 53) are
still
 in
 there (as the area covered by the subfields is not 100%
 equal to
 the
 hippocampus of the aseg).
 How can I remove the remains of the old hippocampal labels?

 Many thanks!
 Best
 Heidi


 ___
 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

[Freesurfer] Questions about beta.nii.gz

2015-10-30 Thread Reza Rajimehr

Hi,

I have two questions:

1) In an fMRI experiment, we have 64 stimulus conditions and a baseline
condition. All conditions are presented in each run. After running the
analysis:

mkanalysis-sess -a category.rh -surface self rh -fsd bold -fwhm 3
-event-related -paradigm paradigm_category.par -nconditions 64 -refeventdur
1 -TR 2 -polyfit 2 -spmhrf 0 -mcextreg -per-run -force

selxavg3-sess -s subj1sess1 -a category.rh

We load beta.nii.gz in Matlab. It has 131546 rows corresponding to the
vertices in rh, and 118 columns. The first 64 columns correspond to the
stimulus conditions that we have. I guess the next 6 columns correspond to
the motion regressors. What are the remaining 48 columns?

2) When we run selxavg3-sess with -run-wise:

selxavg3-sess -s subj1sess1 -a category.rh -run-wise

We have a beta.nii.gz file for each run. But this time, each beta.nii.gz
file has 70 columns. Why the number of columns here is different from that
in the beta file generated without -run-wise?

Thanks for shedding light on this issue!

Reza
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[Freesurfer] bring volumes to fsaverage space

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[Freesurfer] Questions about beta.nii.gz

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