# QSIPrep

QSIPrep is a BIDS App for processing diffusion MRI data.

https://qsiprep.readthedocs.io/

It has 2 workflows:
- pre-processing
- reconstruction

## BIDS

- update IntendedFor - add to dmri-microstructure repo
- make sure epi scans being used as dwi field maps don't have any non b=0 volumes (also remove .bvec and .bval files)

## Pre-processing

#!/bin/bash -l

#SBATCH --partition=high-moby
#SBATCH --array=1-40
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4096
#SBATCH --time=24:00:00
#SBATCH --job-name qsiprep
#SBATCH --output=qsiprep_%j.out
#SBATCH --error=qsiprep_%j.err

STUDY="SPN30"

sublist="/scratch/mjoseph/bids/${STUDY}/code/subject_list.txt"

index() {
   head -n $SLURM_ARRAY_TASK_ID $sublist \
   | tail -n 1
}

BIDS_DIR=/archive/data/${STUDY}/data/bids
OUT_DIR=/archive/data/${STUDY}/pipelines/in_progress
TMP_DIR=/scratch/mjoseph/tmp
WORK_DIR=${TMP_DIR}/${STUDY}/qsiprep
FS_LICENSE=${TMP_DIR}/freesurfer_license/license.txt

SING_CONTAINER=/archive/code/containers/QSIPREP/pennbbl_qsiprep_0.16.0RC3-2022-06-03-9c3b9f2e4ac1.simg

mkdir -p $BIDS_DIR $OUT_DIR $TMP_DIR $WORK_DIR

singularity run \
  -H ${TMP_DIR} \
  -B ${BIDS_DIR}:/bids \
  -B ${OUT_DIR}:/out \
  -B ${WORK_DIR}:/work \
  -B ${FS_LICENSE}:/li \
  ${SING_CONTAINER} \
  /bids /out participant \
  --skip-bids-validation \
  --participant_label `index` \
  --n_cpus 4 --omp-nthreads 2 \
  --freesurfer-input /out/freesurfer \
  --denoise_method dwidenoise \  # MRTrix
  --unringing_method mrdegibbs \ # MRTrix
  --separate_all_dwis \
  --hmc_model eddy \
  --output-resolution 1.7 \ # mandatory
  --fs-license-file /li \
  -w /work \
  --notrack

## Check resolution of input dwi scans

fslinfo
CLZ - resolution is 0.8 or 1

may need to downsample data to get tractography to run

## Distortion Correction

- make sure field maps have IntendedFor tag
- if using T1w for SDC, include both `--use-syn-sdc` and `--force-syn`

## Dealing with different diffusion sampling schemes

- split into separate files
- sub-X_ses-X_acq-21_dwi.nii.gz
- sub-X_ses-X_acq-22_dwi.nii.gz
- sub-X_ses-X_acq-23_dwi.nii.gz
- sub-X_ses-X_acq-multishell_dwi.nii.gz
- dwi in single file

## Updating eddy parameters

# QC Pages

How to share static and dynamic QC pages with others

Examples of good and bad data

## Static

- distortion correction is most important

## Dynamic

https://www.nipreps.org/dmriprep-viewer/#/

- summarize metrics in R report
- look at triplanar view of all volumes
- look at colour FA image

## Reconstruction

### reorient_fslstd

singularity run \
  -H ${TMP_DIR} \
  -B ${BIDS_DIR}:/bids \
  -B ${OUT_DIR}:/out \
  -B ${WORK_DIR}:/work \
  -B ${FS_LICENSE}:/li \
  ${SING_CONTAINER} \
  /bids /out participant \
  --skip-bids-validation \
  --participant_label `index` \
  --n_cpus 4 --omp-nthreads 2 \
  --recon-only \
  --recon-spec reorient_fslstd \
  --recon-input /out/qsiprep \
  --output-resolution 1.7 \
  --fs-license-file /li \
  -w /work \
  --notrack

### DTIFIT

module load FSL/6.0.1
dtifit ....

### TBSS

1.
2.
3.

### amico_noddi

singularity run \
  -H ${TMP_DIR} \
  -B ${BIDS_DIR}:/bids \
  -B ${QSIPREP_DIR}:/qsiprep \
  -B ${OUT_DIR}:/out \
  -B ${WORK_DIR}:/work \
  -B ${FS_LICENSE}:/li \
  ${SING_CONTAINER} \
  /bids /out participant \
  --skip-bids-validation \
  --participant_label `index` \
  --recon-only \
  --recon-spec amico_noddi \
  --recon-input /qsiprep \
  --n_cpus 4 --omp-nthreads 2 \
  --output-resolution 1.7 \
  --fs-license-file /li \
  -w /work \
  --notrack

## Studies that have been run