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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
48 stars 19 forks source link

nonlin masking error #78

Closed juansanchezpena closed 2 years ago

juansanchezpena commented 2 years ago

Dear all, I am running dcanumn/abcd-hcp-pipeline:v0.1.0 on multi band data acquired on a GE Premiere 3T magnet. The ses-21394_task-rest_run-01_nonlin_mask.nii.gz, created during IntensityNormalization is not working for these data and causes erroneous masking downstream in the pre processing. Screen Shot 2022-04-13 at 11 10 37 AM

I am going of HCP 3_22 scripts as the output files from the container do not have enough details.

_${FSLDIR}/bin/fslmaths ${InputfMRI} $biascom $jacobiancom -mas ${BrainMask} -mas ${InputfMRI}_mask -thr 0 -ing 10000 ${OutputfMRI} -odt float if [ X${ScoutInput} != X ] ; then ${FSLDIR}/bin/fslmaths ${ScoutInput} $biascom $jacobiancom -mas ${BrainMask} -mas ${InputfMRI}mask -thr 0 -ing 10000 ${ScoutOutput} -odt float fi

the ses-21394_task-rest_run-01_nonlin.nii.gz, brainmask_fs.2.0.nii.gz and Scout_gdc_mask.nii.gz all look good. Can anyone suggest a possible fix.

TOPUPS: data_type INT16 dim1 90 dim2 90 dim3 60 dim4 2 datatype 4 pixdim1 2.400000 pixdim2 2.400000 pixdim3 2.400000 pixdim4 7.500000

FUNC dim1 90 dim2 90 dim3 60 dim4 375 datatype 4 pixdim1 2.400000 pixdim2 2.400000 pixdim3 2.400000 pixdim4 0.800000 cal_max 0.0000 cal_min 0.0000

juansanchezpena commented 2 years ago

I found the error in acquisition.