Hi Maedeh
in your command line you need a space between the 'n' and the '2', so it
should be:
-n 2
not
-n2
cheers
Bruce
On Mon, 23 Jul 2018, Maedeh Khalilian wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I would like to use the FreeSurfer package to do a parcellation.Just for
testing, I am using
"buckner_data" and there is a step I have been stuck in.I have problem using
"mris_ca_train"
command.This is the whole code I run on my terminal to create my own atlas:
[user@localhost ~]$ export FREESURFER_HOME=/usr/local/freesurfer
[user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
[user@localhost ~]$ export TUTORIAL_DATA=/home/user/Desktop/ramezani/tutorial/
[user@localhost ~]$ export
SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
[user@localhost ~]$ cd $SUBJECTS_DIR
[user@localhost tutorial_subjs]$ mris_ca_train -n2 rh rh.sphere.reg
rh.aparc.annot good_output
./rh.my_atlas.gcs
Usage:
------
mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <subject 2> ...
<output file>
[user@localhost tutorial_subjs]$
As you see it just goes to the next line and doesn't show any errors so I can
get where the problem
is from.
That would be great if you could help me.
Best regards;
Maedeh
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