for meeting with Pearce and Evan: proof-of-concept parent script for PET & T1 coregistration to MNI152

test-epiPETandT1toMNI152.sh

#!/bin/bash

# A short proof-of-concept script for meeting with Pearce and Evan (W, 20130501)
#
# Demonstrates adaptation of existing tools for automated PET->T1->MNI152
# registration. 
#
# INPUT: dicoms for a deidentified participant's T1 and PET sequences.
#
# OUTPUT: PET and T1 nifti volumes nonlinearly registered to MNI152 template (RPI).
# - LH/RH orientation: no fiducial marker. Relying on metadata chains: 
#   DICOM->bxh->NIFTI->NIFTI->NIFTI...
#


#################################################
# step 1/5 - prepare inputs and outputs:
#################################################

subj=tpAuto
inputDirT1Dicoms=~/Downloads/TP_MRI
inputDirPetDicoms=~/Downloads/TP_PET
bxhDir=~/Downloads/bxh_xcede_tools-1.10.7-lsb30.x86_64
tempDir=/tmp
outDir=~/Downloads/TP_outputAutomated
rm -fr /tmp/${subj}*
rm -fr ${outDir}
mkdir ${outDir}


#################################################
# step 2/5 - convert T1 from dicoms to nifti:
#################################################

# ...here we invoke software from FSL and FBIRN:
${bxhDir}/bin/dicom2bxh ${inputDirT1Dicoms}/ser* ${tempDir}/${subj}_t1.bxh
${bxhDir}/bin/bxh2analyze --overwrite --nii ${tempDir}/${subj}_t1.bxh ${tempDir}/${subj}_t1
fslreorient2std ${tempDir}/${subj}_t1.nii* ${outDir}/${subj}_t1.nii


#################################################
# step 3/5 - convert PET from dicoms to nifti:
#################################################

# ...here we invoke software from FSL and FBIRN:
${bxhDir}/bin/dicom2bxh ${inputDirPetDicoms}/ser* ${tempDir}/${subj}_pet.bxh
${bxhDir}/bin/bxh2analyze --overwrite --nii ${tempDir}/${subj}_pet.bxh ${tempDir}/${subj}_pet
fslreorient2std ${tempDir}/${subj}_pet.nii* ${outDir}/${subj}_pet.nii



#################################################
# step 4/5 - coregister PET and T1 to MNI152 template:
#################################################

# invoking a longer pre-existing script of mine that uses FSL to do the heavy
# lifting (bet for skull strip, flirt and fnirt for linear and nonlinear
# registration. Source code for that script:  http://goo.gl/R0dpy ):
bash ~/brainwhere/registerTo1mmMNI152.sh \
-s ${subj} \
-t ${outDir}/${subj}_t1.nii* \
-o ${outDir} \
-e ${outDir}/${subj}_pet.nii*


#################################################
# step 5/5 - display the results interactively in fslview:
#################################################
fslview ${outDir}/*warp* &