Preprocessing T1 and T2 Images

https://slides.com/njhunsak/preprocessing-t1-images-part1

https://slides.com/njhunsak/preprocessing-t1-images-part2

antsRegistrationSyNQuick.sh \
-d 3 \
-f ${DERIV}/${SUBJ})${SES}_T1w.nii.gz \
-m ${BIDS}/${SUBJ}_${SES}_T2w.nii  \
-o ${DERIV}/${SUBJ}_${SES}_inplaneT2 \
-t a

You can find preprocessed T1 and T2 data under the derivatives directory located in each BIDS organized dataset:

STUDY_DIR/
|–– derivatives/
    |–– pT1T2/
        |–– sub-001_ses-1/
            |–– sub-001_ses-1_T1w.nii.gz
            |–– sub-001_ses-1_inplaneT2w.nii.gz
        |–– sub-001_ses-2/
            |–– sub-001_ses-2_T1w.nii.gz
            |–– sub-001_ses-2_inplaneT2w.nii.gz
|–– sub-001/
|–– sub-002/
|–– sub-003/
participants.tsv
dataset_description.json