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 <fis...@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 >> >> >> >> >> >> >> >> > > 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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