add proprocess-nifti.sh

scripts/README.md

@@ -2,3 +2,5 @@
 These scripts can be helpfull while you use the cat12 pipeline
 ## check.sh
 Check if all files are created. See usage with `$ ./check.sh --help`
+## preprocess-nifti.sh
+Allows to quickly process a nifti when your pipeline is set up. Please adjust the variables on top of the script to your needs. Afterwards usage is easy with: `$ ./preprocess-nifti.sh <path_to_nifti>`. This script creates a working directory, derives a batch file from the template and then starts the pipeline for this nifti. Only works for one nifti file!

scripts/preprocess-nifti.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# Usage: ./preprocess-nifti.sh <path_to_nifti>
+# Author: Kelvin Sarink <[email protected]>
+
+
+# Edit the following variables to your needs:
+path_to_compiled_spm="/scratch/tmp/e0trap/software/cat12_joint_pipeline/ksarink-cjp_v0008-spm12_v7771-cat12_r1720/"
+path_to_mcr="/scratch/tmp/e0trap/software/mcr/v96"
+path_to_batch_template="/scratch/tmp/e0trap/software/cat12_joint_pipeline/cat12_complete_joint_pipeline.mat"
+
+# path_which_needs_to_be_replaced does not need to be changed as long as you use cjp8
+path_which_needs_to_be_replaced="/spm-data/Scratch/spielwiese_kelvin/cat12_joint_pipeline/cjp_v0008-spm12_v7771-cat12_r1720-modifiedcatdefaults/"
+
+
+
+# Do not edit anything below:
+[ -z "$1" ] && exit 1
+nifti=`realpath $1`
+id=`basename $nifti | sed 's|.nii||g'`
+timestamp=`date +'%Y-%m-%d_%H-%M-%S'`
+workingdir="./workingdir/${id}_$timestamp"
+mkdir -p $workingdir
+workingdir=`realpath $workingdir`
+cd $workingdir
+
+export MCR_INHIBIT_CTF_LOCK=1
+
+
+batchfilename=$workingdir/${id}-spm12batch.mat
+#Create SPM12 batch 
+$path_to_compiled_spm/run_spm12.sh \
+$path_to_mcr \
+adjust_input \
+$path_to_batch_template \
+$batchfilename \
+$nifti \
+$path_which_needs_to_be_replaced &> ./adjusting.log;
+
+#Execute SPM12 batch
+$path_to_compiled_spm/run_spm12.sh \
+$path_to_mcr \
+batch $batchfilename &> ./spm12.log