Commit c2c64939 authored by Brent Womble's avatar Brent Womble
Browse files

Fixed syntax after troubleshooting. Jobs actually run now.

parent 91e3c730
......@@ -4,7 +4,7 @@
function cheaha_vessels_segment(sub_dir, sub)
%Segment in SPM12 using modified TPMs, input should be a directory and a subject ID
%Add SPM12 and Nifti tools to the path
%Add SPM12 to the path
addpath('/share/apps/vbc/matlab/toolbox/spm12');
sub_folder = [sub_dir,'/',sub,'/'];
......@@ -48,3 +48,6 @@ matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 1;
matlabbatch{1}.spm.spatial.preproc.warp.write = [0 0];
spm_jobman('initcfg');
spm_jobman('run',matlabbatch);
#!/bin/bash
jobs=/data/scratch/kecannon/brainhack2018/HCP_jobs1
jobs=/data/scratch/kecannon/brainhack2018/jobs1_HCP
sub_dir=/data/scratch/kecannon/brainhack2018/HCP
mkdir $jobs
cd $sub_dir
for sub in `find 99*`
for sub in `find 99* -type d`
#Test with 6 folders
do
......@@ -13,15 +13,13 @@ do
cat > $jobs/segment_$sub.sh <<EOF
#!/bin/bash
cd $sub_dir/$subject/
module load rc/matlab/R2013a
matlab -nodesktop -nosplash -r "cheaha_vessels_segment('$sub_dir','$sub')"
EOF
done
for sub in `find 99*`
for sub in `find 99* -type d`
#Test with 6 folders
do
......
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