Hi Ting
if you can't see the share folder then you can't access our binaries.
Maybe talk to your local sysadmins?
cheers
Bruce
On Sat, 20 Jan 2018, Ting Li wrote:
Hi Bruce,
Thanks for your quickly response. Sorry for my late.
I try to run FreeSurfer in a server. It was installed in my home share folder.
Here is the setting
environment information.
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/share/freesurfer
FSFAST_HOME /home/share/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/share/freesurfer/subjects
MNI_DIR /home/share/freesurfer/mni
And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
When I do a ls, I can’t see the share folder. Do you think I should install if
under /home/ting instead of /home/share?
Thanks a lot!
Best,
Ting
On Jan 20, 2018, at 9:12 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Ting
that means $FREESURFER_HOME/bin is not in your path and you need to add it
(and make sure that the environment variable FREESURFER_HOME is set
properly). If it is, you can do:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
Are you new to Linux also? If so, you might want to go through some basic
tutorials.
cheers
Bruce
On Fri, 19 Jan 2018, Ting Li wrote:
Hi Freesurfer Expert,
I am very new to Freesurfer and have a very basic question. How to
convert
.nii files to nii.gz? I have tried the mri_convert subject_name.nii
to
subject_name.nii.gz directly. It gives me an error information that
mri_convert: command not found. Thanks for your help!
Best,
Ting
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