Minipig landmark Initializations

[hjmjohnson]

Use landmark initialization to generate a starting point for registering mini-pigs to human brains.

Script to perform landmark registration

#!/bin/bash
# \author Hans J. Johnson
# Script to test BRAINSLandmarkInitializer in preparation for ANTs
# MALF based segmentations.

FLMKFILE="$(pwd)/sub-Ada165/ses-20130321/sub-Ada165_ses-20130321_run-094402_T1w_2_markup.fcsv"
MLMKFILE="$(pwd)/sub-Adelheid313/ses-20160801/sub-Adelheid313_ses-20160801_run-102230_T1w_markup.fcsv"
WTSFILE="$(pwd)/mplmk.wts"

# module load BRIANSTools/201904??
BINDIR=/Users/johnsonhj/src/BT-11/bin

TFMTYPE=AffineTransform
#TFMTYPE=VersorRigid3DTransform

M2F_TFM="$(pwd)/Adelheid313-20160801_2_Ada165-20130321_${TFMTYPE}.h5"

INTERPMODE=Linear
if [[ ${TFMTYPE} ==  "VersorRigid3DTransform" ]]; then
  INTERPMODE=ResampleInPlace
fi

${BINDIR}/BRAINSLandmarkInitializer \
   --inputMovingLandmarkFilename "${MLMKFILE}" \
   --inputFixedLandmarkFilename "${FLMKFILE}" \
   --inputWeightFilename "${WTSFILE}" \
   --outputTransformType ${TFMTYPE} \
   --outputTransformFilename "${M2F_TFM}"

FIMGFILE="$(pwd)/sub-Ada165/ses-20130321/sub-Ada165_ses-20130321_run-094402_T1w.nii"
MIMGFILE="$(pwd)/sub-Adelheid313/ses-20160801/sub-Adelheid313_ses-20160801_run-102230_T1w.nii"
OUTFILE="$(pwd)/warped_${TFMTYPE}_sub-Adelheid313_ses-20160801_run-102230_T1w.nii"

${BINDIR}/BRAINSResample \
   --interpolationMode ${INTERPMODE} \
   --warpTransform "${M2F_TFM}" \
   --pixelType short \
   --outputVolume "${OUTFILE}" \
   --inputVolume "${MIMGFILE}" \
   --referenceVolume "${FIMGFILE}"
#  --inverseTransform \

echo lsl "${OUTFILE}"  "${FIMGFILE}"

[KKnoernschild]

I do not see the weight file, and then script errors out since the .h5 file is not already created.

[hjmjohnson]

Sorry,
Here is a zipped version of that file:

mplmk.wts.zip