Hi,
I am using QSIPrep 1.0.1 with Singularity to preprocess a 258-volume DSI dataset. However, I discovered that I could not use DSI Studio to track fibers from the preprocessed data, as it appears the bvec file generated during preprocessing contained errors. To resolve this, I had to apply a Y-axis flip to obtain correct fiber tracking results. Could this discrepancy stem from a coordinate system mismatch? The issue appears to result from incompatible spatial orientation conventions between the preprocessing pipeline and tracking software.
Code
singularity run --cleanenv \
-B $wd/sub-$subj:/wd \
-B $bids:/bids \
-B $output:/output \
-B $fs_license:/fs_license \
-B $templateflow:$templateflow \
/ibmgpfs/cuizaixu_lab/xulongzhou/apps/singularity/qsiprep-1.0.1.sif \
/bids /output participant -w /wd \
--n-cpus 6 --omp-nthreads 6 --mem-mb 120G \
--participant-label sub-$subj \
--fs-license-file /fs_license/license.txt \
--skip-bids-validation \
--subject-anatomical-reference sessionwise \
--anat-modality T1w \
--ignore fieldmaps \
--unringing-method mrdegibbs \
--output-resolution 2 \
--hmc-model 3dSHORE \
--use-syn-sdc error \
--force-syn \
--stop-on-first-crash \
--resource-monitor \
--notrack
