you don't need to supply the full path to the inputs of mris_preproc, but you must for the output of mris_preproc as well as the input and output of surf2surf and glmfit

On 11/28/13 1:25 PM, Laura Taylor wrote:

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 mailto: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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