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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