concatenating TransformParameters files

[amwink]

Hi all, I have a question about combining multiple TransformParameters files into 1 operation.

The script that I have cycles over a number of subjects, all of whom have a PET image and an MR scan, each in their own space. Every PET needs to be registered to the MR, the MR to an MNI template, and then the PET to MNI via the MR.

So given

PETFILE=<native-space PET>
PET_INPUT_DIR=<directory PETFILE>
PET_OUTPUT_DIR=<directory mni-space PET>
PET_OUTPUTFILE=<mni-space PET>

and

MRIFILE=<native-space T1w>
MRI_INPUT_DIR=<directory MRIFILE>
MRI_OUTPUT_DIR=<directory mni-space T1w>
MRI_OUTPUTFILE=<mni-space T1w>
TEMPLATE=$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

I first do

elastix -f $MRIFILE -m $PETFILE -out $PET_OUTPUT_DIR -p Parameters_Rigid.txt -p Parameters_Affine.txt
transformix -in $PETFILE -out $PET_OUTPUT_DIR -tp ${PET_OUTPUT_DIR}/TransformParameters.1.txt
mv $PET_OUTPUT_DIR/result.nii.gz ${PET_OUTPUTFILE//_pet.nii/_space-T1w_pet.nii}

and

elastix -f $TEMPLATE -m $MRIFILE -out $MRI_OUTPUT_DIR -p Parameters_Rigid.txt -p Parameters_Affine.txt -p Parameters_BSpline.txt
transformix -in $MRIFILE -out $MRI_OUTPUT_DIR -tp ${MRI_OUTPUT_DIR}/TransformParameters.2.txt
mv $MRI_OUTPUT_DIR/result.nii.gz ${MRI_OUTPUTFILE//_T1w.nii/_space-mni.nii} 

to register PET to MR and MR to MNI (the transformix calls are not strictly necessary but will be used later), both of which work as expected.

My cunning plan to warp the PET to MNI in 1 go was to change the line (InitialTransformParametersFileName "NoInitialTransform") in the MR rigid transform parameter file to (InitialTransformParametersFileName "${PET_OUTPUT_DIR}/TransformParameters.1.txt") as explained in section 4.3 of the manual, so the initial parameters of the transform to warp the MR to MNI are now the final parameters for registering the PET to the MR.
However, when I do that and apply the resulting transform to the PET:

sed $MRI_OUTPUT_DIR/TransformParameters.0.txt -e s#\"NoInitialTransform\"#\"${PET_OUTPUT_DIR}/TransformParameters.1.txt\"# > $MRI_OUTPUT_DIR/TransformParameters.0_PET.txt
transformix -in $PETFILE -out $PET_OUTPUT_DIR -tp ${MRI_OUTPUT_DIR}/TransformParameters.2.txt
mv $PET_OUTPUT_DIR/result.nii.gz ${PET_OUTPUTFILE//_pet.nii/_space-mni_pet.nii}			

the resulting is not registered correctly to the MNI template.

However, if instead I keep the MR transform parameters intact and apply them to the PET that was resampled in the MR space,

transformix -in ${PET_OUTPUTFILE//_pet.nii/_space-T1w_pet.nii} -out $PET_OUTPUT_DIR -tp ${MRI_OUTPUT_DIR}/TransformParameters.2.txt;
mv $PET_OUTPUT_DIR/result.nii.gz ${PET_OUTPUTFILE//_pet.nii/_desc-resampled2x_space-mni_pet.nii} 

the result is correctly registered to the MNI space.

Am I forgetting something for combining the two sets of TransformParameters.txt files?

Or could the problem be that using TransformParameters.1.txt from the PET-to-MR registration (affine) as an initial transform in TransformParameters.0.txt from the MR-to-MNI registration (rigid) discards a number of parameters?