Thanks, Bruce...

Do you know if you also have to specify the full path for the location of input and output files in mris_preproc, mri_surf2surf, and mri_glmfit?

By default, when I ran the above programs, my output files were placed in my computers home directory and not my freesurfer home directory (I did not specify full pathnames).

However, mris_preproc seemed to be able to read in my target (--target) (fsaverage) without needing a full pathname, and mri_surf2surf also seemed to be able to read in my subject (--s) without needing a full pathname.

Please let me know if I have this right (especially regarding reading in input files).

Thank you,

Laura

On Wed, Nov 27, 2013 at 11:53 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Laura

freeview by default doesn't use any of the environment variables. You need to give it the full path to the data you are trying to visualize. It included your home dir in the path probably because that was your pwd.

cheers
Bruce

On Wed, 27 Nov 2013, Laura Taylor wrote:

Hi,

I previously installed set-up and have successfully used freesurfer to run
recon-all and visualize my results in tkmedit and tksurfer. However when I
went to analyze my data and also view it in freeview I have run into a
problem with what my home directory is considered for these applications.

When I try and load images in freeview from the command line I get the
following error:

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Data/freesurfer
FSFAST_HOME       /Data/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Data/freesurfer/subjects
MNI_DIR           /Data/freesurfer/mni
woodward@Bambi:~$ freeview -v B60/mri/braimmask.mgz
mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not open file
MRIread failed: Unable to read from /home/woodward/B60/mri/braimmask.mgz
mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not open file

This is because freeview is looking for my subject in the computers home
directory (~) which is /home/woodward.

I get a similar problem when I run i.e. mri_glmfit. When I specify

--glmdir lh.dx_age.glmdir, it places the output in my home (~)
(/home/woodward) directory and not in my FREESURFER_HOME directory.
mris_preproc and mri_surf2surf also seems to be placing their output in my
computers home directory.

I've looked in FreeSurferEnv.sh and I can't seem to find a place to make any
changes. Please let me know if I can edit a path somewhere, or if I need to
write out the full path for the mri_* programs and freeview.

Thank you,

Laura

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