Re: [Freesurfer] subject directory

2017-03-17 Thread Douglas N Greve
edu> > *Reply-To: *Freesurfer support list > > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Date: *Thursday, March 9, 2017 at 10:45 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" > <mailto:freesurfer@nmr.mgh.harvard.edu>

Re: [Freesurfer] subject directory

2017-03-17 Thread Dr. M. Shahid
/limachi/freesurfer/subjects/CON_202/surf/lh. > thickness.fwhm10.fsaverage.mgh > > > > Thanks, > > > Gaurang > > > > *From: *Douglas Greve > *Reply-To: *Freesurfer support list > *Date: *Sunday, March 12, 2017 at 6:56 PM > > *To: *"freesurfer@n

Re: [Freesurfer] subject directory

2017-03-15 Thread Limachia, Gaurang (NIH/NINDS) [F]
edu" Subject: Re: [Freesurfer] subject directory Can you send the entire terminal output (not just the error) On 3/10/17 4:01 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: The error is ERROR: cannot find /home/username/freesurfer/subjects/surf/lh.thickness.fwhm10.fsaverage.mgh However,

Re: [Freesurfer] subject directory

2017-03-12 Thread Douglas Greve
/subjects/… I don’t know why it tries to find the files in the default home/… folders. Thanks, Gaurang *From: *Douglas Greve *Reply-To: *Freesurfer support list *Date: *Thursday, March 9, 2017 at 10:45 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] subject dire

Re: [Freesurfer] subject directory

2017-03-10 Thread Limachia, Gaurang (NIH/NINDS) [F]
Reply-To: Freesurfer support list Date: Thursday, March 9, 2017 at 10:45 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] subject directory can you send the terminal entire output that includes the error? On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear

Re: [Freesurfer] subject directory

2017-03-10 Thread Bruce Fischl
Hi Gaurang you need to send us the full screen output of what you ran. And what do you mean by "customize"? Did you change the subject dir after running recon-all? cheers Bruce On Fri, 10 Mar 2017, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear Freesurfer Experts,   I want to customize t

Re: [Freesurfer] subject directory

2017-03-09 Thread Douglas Greve
can you send the terminal entire output that includes the error? On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaver

[Freesurfer] subject directory

2017-03-09 Thread Limachia, Gaurang (NIH/NINDS) [F]
Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh However, after running this command it keeps checking

Re: [Freesurfer] subject directory error: can't find subject

2016-10-24 Thread Douglas N Greve
Try setting SUBJECTS_DIR to the full path rather than just ./ On 10/21/2016 03:03 PM, Russ, Brian (NIH/NIMH) [E] wrote: > Hi, > > I’m attempting to use FreeSurfer to create a set of surface and flat maps for > use with some macaque data. Using a number of programs prior to FreeSurfer I > have

[Freesurfer] subject directory error: can't find subject

2016-10-21 Thread Russ, Brian (NIH/NIMH) [E]
Hi, I’m attempting to use FreeSurfer to create a set of surface and flat maps for use with some macaque data. Using a number of programs prior to FreeSurfer I have created a skull-stripped T1 image and White Matter mask and then successfully used FreeSurfers mksubjdirs, mri_convert, mri_fill,