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
<fis...@nmr.mgh.harvard.edu <mailto: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
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