Hello all, I am trying to create a template for longitudinal processing and am running into some problems generating the file. I have many subjects so I am running a batch script. I am using version 5.1.0
Any suggestions?
Thanks! Corinna
Here is my script: #!/bin/tcsh setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template
set subjects=`cat $1`
foreach subject ($subjects)
echo "-------------------- Processing $subject -------------------------" set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/ set template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri set tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz set tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz set tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz set tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz #set nu_mgz=${subj_dir}/mri/nu.mgz
recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos} -tp ${tp_24mos} -tp ${tp_36mos} -all
end
Here is my output: -------------------- Processing 137_S_0631 ------------------------- Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/corinna/ADNI/template Actual FREESURFER_HOME /Applications/freesurfer Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012 /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template \n mri_robust_template --mov /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz --lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta --template /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz --average 1 --sat 4.685 \n $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. Total: 4 input volumes --lta: Will output LTA transforms --template: Using /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'... mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz, -1): could not open file MultiRegistration::loadMovables: could not open input volume /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz.
Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
recon-all -s 137_S_0631_template exited with ERRORS at Mon May 14 18:21:23 EDT 2012
For more details, see the log file /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting