Hi all, I'm having trouble getting anything through on 5.1 using scripts, although I can run recon-all at the commandline. I'm running freesurfer on a remote cluster, not locally. Specifics of the cluster itself aside, with 5, I could run:
*vbbatch -c * *"PATH=$PATH:/usr/local/freesurfer_64bit_5; export PATH; * *FREESURFER_HOME=/usr/local/freesurfer_64bit_5; export FREESURFER_HOME; * *SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects; export SUBJECTS_DIR;** * *recon-all -i SW419_Day1.mgz -subject SW419Day1_fullrecon -all" -d1 -r* With 5.1, I have to specify MINC_BIN_DIR within this command (get an error if I don't, saying that it's not defined) and I still get stuck in the talairach transform, with: mritotal -verbose -debug -clobber -modeldir /../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22637/src.mnc transforms/talairach.auto.xfm mritotal: Command not found. Clearly mritotal is working if recon-all at the commandline works. Do I need to specify more environmental variables somewhere for 5.1? I've tried specifying MINC_BIN_DIR, MINC_LIB_DIR, and MNI_DIR in the command as well, with no luck. My bash profile includes: PATH=$PATH:/usr/local/freesurfer5-1/bin FREESURFER_HOME=/usr/local/freesurfer5-1 SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects MINC_BIN_DIR=/usr/local/freesurfer5-1/mni/bin MINC_LIB_DIR=/usr/local/freesurfer5-1/mni/lib PERL5LIB=/usr/local/freesurfer5-1/mni/lib/perl5/5.8.5 MNI_DIR=/usr/local/freesurfer5-1/mni FSFAST_HOME=/usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT=nii And on startup I see: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer5-1 FSFAST_HOME /usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /jet/kable/CorticalThickness/Subjects MNI_DIR /usr/local/freesurfer5-1/mni FSL_DIR /usr/local/fsl thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371
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