recon-all -s <subj> -localGI

List overview All Threads
Download

newer

older

Longitudinal base creating in...

dimensions of the segmented MRI

André Schmidt

13 Dec 2016 13 Dec '16

10:10 a.m.

Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

Attachments:

attachment.html (text/html — 3.0 KB)

Show replies by date

Douglas Greve

13 Dec 13 Dec

10:26 a.m.

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote:

...

Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

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

André Schmidt

11:16 a.m.

Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 81473 Dec 13 17:09 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Dec 13 17:22:19 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 16:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote: Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

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

Douglas Greve

4:53 p.m.

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote:

...

Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 81473 Dec 13 17:09 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Dec 13 17:22:19 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] *Gesendet:* Dienstag, 13. Dezember 2016 16:26 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] recon-all -s <subj> -localGI

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote:

...
Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

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

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

André Schmidt

14 Dec 14 Dec

7:14 a.m.

Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

Andres-MacBook-Pro:~ andre$ echo $PATH /Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Andres-MacBook-Pro:~ andre$ PATH=/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/matlab/MATLAB_R2014a.app/bin/matlab Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 130383 Dec 14 11:44 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec 14 13:15:53 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.h...

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote: Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 16:26 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote: Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

Douglas Greve

11:03 a.m.

What happens if you run getmatlab ?

On 12/14/16 7:14 AM, André Schmidt wrote:

...

Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

Andres-MacBook-Pro:~ andre$ echo $PATH /Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Andres-MacBook-Pro:~ andre$ PATH=/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/matlab/MATLAB_R2014a.app/bin/matlab Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 130383 Dec 14 11:44 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec 14 13:15:53 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.h...

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] *Gesendet:* Dienstag, 13. Dezember 2016 22:53 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote:

...
Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 81473 Dec 13 17:09 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Dec 13 17:22:19 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] *Gesendet:* Dienstag, 13. Dezember 2016 16:26 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] recon-all -s <subj> -localGI

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote:

...
Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

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

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

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

André Schmidt

11:13 a.m.

I get the following:

Andres-MacBook-Pro:subjects andre$ getmatlab ERROR: Cannot find matlab. Does not exist or is not in path.

I guess adding the path (or what I defined as path) didn't work.

Bw André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 14. Dezember 2016 17:03 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

What happens if you run getmatlab ?

On 12/14/16 7:14 AM, André Schmidt wrote: Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote: Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote: Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

dgw

11:27 a.m.

André,

It looks like you have the matlab path typed correctly. I would try to tab complete it in a terminal to check. You currently have it typed as this: /Applications/matlab/MATLAB_R2014a.app/bin/matlab I expect it to be this on your computer: /Applications/MATLAB_R2014a.app/bin/matlab

Try doing it through tab complete. then hit enter, if matlab opens that is the correct path to add.

hth d

On Wed, Dec 14, 2016 at 11:13 AM, André Schmidt andre.schmidt@unibas.ch wrote:

...

I get the following:

Andres-MacBook-Pro:subjects andre$ getmatlab ERROR: Cannot find matlab. Does not exist or is not in path.

I guess adding the path (or what I defined as path) didn't work.

Bw André

Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 14. Dezember 2016 17:03

An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

What happens if you run getmatlab ?

On 12/14/16 7:14 AM, André Schmidt wrote:

Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

Andres-MacBook-Pro:~ andre$ echo $PATH /Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Andres-MacBook-Pro:~ andre$ PATH=/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/matlab/MATLAB_R2014a.app/bin/matlab Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 130383 Dec 14 11:44 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Dec 14 13:15:53 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.h...

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote:

Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl/fsl Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 andre staff 81473 Dec 13 17:09 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subj001/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Dec 13 17:22:19 GMT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 16:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote:

Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

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

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

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

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

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

André Schmidt

11:40 a.m.

Finally, I was able to add the path: export PATH=$PATH:/Applications/matlab/MATLAB_R2014a.app/bin/ Unfortunately, I receive a new error:

ERROR: make_roi_paths did not complete successfully!

Do you know what happened now? To compute LGI, I just use the rh.pial and lh.pial from recon-all <subjid> all (only these two files are in the surf directory). Do I need all files from recon-all <subjid> all?

Many thanks for your help again André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 14. Dezember 2016 17:03 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

What happens if you run getmatlab ?

On 12/14/16 7:14 AM, André Schmidt wrote: Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote: Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote: Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

André Schmidt

11:50 a.m.

Or more precisely (sorry for all the emails):

Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);

EDU>> ERROR: make_roi_paths did not complete successfully!

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "André Schmidt [andre.schmidt@unibas.ch] Gesendet: Mittwoch, 14. Dezember 2016 17:40 An: Freesurfer support list Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Finally, I was able to add the path: export PATH=$PATH:/Applications/matlab/MATLAB_R2014a.app/bin/ Unfortunately, I receive a new error:

ERROR: make_roi_paths did not complete successfully!

Many thanks for your help again André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 14. Dezember 2016 17:03 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

What happens if you run getmatlab ?

On 12/14/16 7:14 AM, André Schmidt wrote: Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

I am still receiving the same error message. Do you have another clue what is going wrong here? Best wishes André

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote: Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working? Thanks again and best wishes André

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote: Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help! Best wishes André

3457

Age (days ago)

3458

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

9 comments

3 participants

tags (0)

participants (3)

André Schmidt
dgw
Douglas Greve