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