Carl Helmick

> It sounds like the environment variable "SINGULARITY_BINDPATH" might be set on your system. This tells singularity to auto-bind specific paths into your container. For example: export SINGULARITY_BINDPATH="/opt,/scratch" would mount...

> Reference shape: > (106, 106, 70) > Image shape: > (106, 106, 70, 40) Hi @mattcieslak, I'm having the same issue as @IRuotsa. Our input dwi data has 2...

Hi @mattcieslak, As you suggested, I moved the 8-dir reverse-PE over to the /fmap/ directory with the "IntendedFor". The test-job is still running, but it has now gone well past...

Something like this should work (bash-code example): ``` #!/bin/bash export ANTSPATH=/opt/ants-2.4.2/bin export PATH="$ANTSPATH:$PATH" PROJECT_DIR=/project/BIDS_WORK S="sub-001" les_img=$PROJECT_DIR/BIDS_defaced/$S/anat/${S}_T1w_label-lesion_roi.nii.gz QSI_DIR=$PROJECT_DIR/derivs/qsiprep/$S/anat ref_img=$QSI_DIR/${S}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz xfm_file=$QSI_DIR/${S}_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 out_img=$QSI_DIR/${S}_space-MNI152NLin2009cAsym_label-lesion_roi.nii.gz ${ANTSPATH}/antsApplyTransforms \ --dimensionality 3 \ --interpolation NearestNeighbor \ --reference-image ${ref_img}...

@mattcieslak Interesting! I tested my script on a couple of datasets and you are indeed correct, the registrations are missing the T1wNative-to-T1wACPC rigid-body transform. I had originally only tested it...

@galambda Your file naming doesn't seem to match the actual image contrast. For example, your sub-KM1001_ses-1_T1w.nii.gz looks like a T2w image. Correct filenaming will allow MRIQC to use the contrast-specific...