Fixed syntax after troubleshooting. Jobs actually run now.

cheaha_vessels_segment.m

@@ -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);

cheaha_vessels_segment.sh

 #!/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