Dsi_studio_gqi expected outputs using QSIRecon

Software Support
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1

Summary of what happened:

I ran qsirecon for dsi_studio_gqi on HPC for 1 subject and received no errors and received outputs. Am I missing outputs from this? I am not sure how many I should have, looking at the read the docs. Should I have all of these outputs?

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My outputs in derivatives folder sub-01 dwi directory include:

(base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev$ cd qsirecon_dev_dsi_studio_gqi/
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi$ ls
atlases  dataset_description.json  derivatives  logs  sub-01
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi$ cd sub-01/
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi/sub-01$ ls
dwi  log
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi/sub-01$ cd dwi/
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi/sub-01/dwi$ ls
sub-01_run-01_space-ACPC_seg-4S256Parcels_dseg.mif.gz  sub-01_run-01_space-ACPC_seg-4S256Parcels_dseg.nii.gz  sub-01_run-01_space-ACPC_seg-4S256Parcels_dseg.txt

My qsiprep outputs being pulled are as follows:

(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsiprep_dev_v1.0.1$ ls
dataset_description.json  sub-04       sub-09       sub-13       sub-17       sub-21       sub-25       sub-31       sub-35       sub-39       sub-43       sub-47
logs                      sub-04.html  sub-09.html  sub-13.html  sub-17.html  sub-21.html  sub-25.html  sub-31.html  sub-35.html  sub-39.html  sub-43.html  sub-47.html
sub-01                    sub-05       sub-10       sub-14       sub-18       sub-22       sub-26       sub-32       sub-36       sub-40       sub-44       sub-48
sub-01.html               sub-05.html  sub-10.html  sub-14.html  sub-18.html  sub-22.html  sub-26.html  sub-32.html  sub-36.html  sub-40.html  sub-44.html  sub-48.html
sub-02                    sub-06       sub-11       sub-15       sub-19       sub-23       sub-29       sub-33       sub-37       sub-41       sub-45
sub-02.html               sub-06.html  sub-11.html  sub-15.html  sub-19.html  sub-23.html  sub-29.html  sub-33.html  sub-37.html  sub-41.html  sub-45.html
sub-03                    sub-08       sub-12       sub-16       sub-20       sub-24       sub-30       sub-34       sub-38       sub-42       sub-46
sub-03.html               sub-08.html  sub-12.html  sub-16.html  sub-20.html  sub-24.html  sub-30.html  sub-34.html  sub-38.html  sub-42.html  sub-46.html
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsiprep_dev_v1.0.1$ cd sub-01
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsiprep_dev_v1.0.1/sub-01$ ls
anat  dwi  figures  log
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsiprep_dev_v1.0.1/sub-01$ cd dwi
(puma) (base) xkg@/xdisk/karpjf/xkg/derivatives/darpa_dev/qsiprep_dev_v1.0.1/sub-01/dwi$ ls
sub-01_run-01_desc-confounds_timeseries.tsv            sub-01_run-01_space-ACPC_desc-preproc_dwi.bval    sub-01_run-01_space-ACPC_dwiref.nii.gz
sub-01_run-01_space-ACPC_desc-brain_mask.nii.gz        sub-01_run-01_space-ACPC_desc-preproc_dwi.bvec    sub-01_run-01_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-01_run-01_space-ACPC_desc-image_qc.tsv             sub-01_run-01_space-ACPC_desc-preproc_dwi.json    sub-01_run-01_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-01_run-01_space-ACPC_desc-preproc_dwi.b            sub-01_run-01_space-ACPC_desc-preproc_dwi.nii.gz
sub-01_run-01_space-ACPC_desc-preproc_dwi.b_table.txt  sub-01_run-01_space-ACPC_desc-slice_qc.json

Command Used

#!/bin/bash

############################################################
############# BEGIN SLURM CONFIGURATION ######################

#SBATCH --partition=standard
#SBATCH --time=22:00:00
#SBATCH --nodes=2 --ntasks=24
#SBATCH --job-name=qsirecon
#SBATCH --account=karpjf
#SBATCH --mail-type=ALL
#SBATCH --mail-user=xkg@arizona.edu

#SBATCH --array=0

############################################################
############## BEGIN SCRIPT TO RUN #########################

# ENVIRONMENT VARIABLES
export SIF=/contrib/singularity/shared/neuroimaging
export APP=${SIF}/qsirecon_v1.1.0.sif

# Set main project directory
export MRIS=/xdisk/karpjf/xkg

# Point to the preprocessed data and freesurfer outputs
export APP_PREP_DERIV_DIR=${MRIS}/derivatives/darpa_dev/qsiprep_dev_v1.0.1
export FREESURFER_DIR=${MRIS}/derivatives/darpa_dev/fmriprep_dev_v24.1.1/sourcedata/freesurfer
export LICENSE=/groups/dkp/neuroimaging/license.txt

# Define the recon spec for this workflow
export RECON_SPEC=dsi_studio_gqi

# Define output and work directories
export APP_DERIV_DIR=${MRIS}/derivatives/darpa_dev/qsirecon_dev_dsi_studio_gqi
export WORK_DIR=${MRIS}/work/darpa_work/${RECON_SPEC}

# TEMPLATEFLOW setup
export TEMPLATEFLOW_HOME=/groups/dkp/neuroimaging/templateflow
export APPTAINTERENV_TEMPLATEFLOW_HOME=/opt/templateflow

# SUBJECT ARGUMENT
# Subject=${sub}
# Get subject ID from list using SLURM array index
Subject=$(sed -n "$((SLURM_ARRAY_TASK_ID + 1))p" /xdisk/karpjf/xkg/scripts/darpa_subjects_clean.txt)

if [ -z "${Subject}" ]; then
  echo "ERROR: Subject ID could not be determined. Please check SLURM_ARRAY_TASK_ID and subject list."
  exit 1
fi

if [ ! -d ${APP_DERIV_DIR} ]; then 
    mkdir -p ${APP_DERIV_DIR}
fi

# Create necessary directories if not present
if [ ! -d ${APP_DERIV_DIR} ]; then 
    mkdir -p ${APP_DERIV_DIR}
fi

if [ ! -d ${WORK_DIR} ]; then 
    mkdir -p ${WORK_DIR}
fi

# Run qsirecon with apptainer
apptainer run \
  --containall --writable-tmpfs \
  --bind ${TEMPLATEFLOW_HOME}:${APPTAINTERENV_TEMPLATEFLOW_HOME} \
  --bind ${MRIS} \
  --bind "${LICENSE}:/license.txt" \
  ${APP} \
  ${APP_PREP_DERIV_DIR} \
  ${APP_DERIV_DIR} \
  participant \
  --participant-label ${Subject} \
  --stop-on-first-crash \
  --recon-spec ${RECON_SPEC} \
  --output-resolution 1.0 \
  --input-type qsiprep \
  --fs-license-file /license.txt \
  --fs-subjects-dir "${FREESURFER_DIR}" \
  -w "${WORK_DIR}" \
  --nprocs 24 \
  --omp-nthreads 8 \
  --atlases 4S256Parcels \
  -v -v

# Echo the command for logging

echo ""
echo "this is the command that was run:"
echo "apptainer run --containall --writable-tmpfs --bind ${TEMPLATEFLOW_HOME}:${APPTAINTERENV_TEMPLATEFLOW_HOME} --bind ${MRIS} --bind \"${LICENSE}:/license.txt\" ${APP} ${APP_PREP_DERIV_DIR} ${APP_DERIV_DIR} participant --participant-label ${Subject} --stop-on-first-crash --recon-spec ${RECON_SPEC} --output-resolution 1.0 --input-type qsiprep --fs-license-file /license.txt --fs-subjects-dir \"${FREESURFER_DIR}\" -w \"${WORK_DIR}\" --nprocs 24 --omp-nthreads 8 --atlases 4S256Parcels -v -v"

# Rename SLURM output
mv slurm-${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID}.out ${MRIS}/slurm.out/slurm_qsirecon-${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID}_${RECON_SPEC}.txt

Version:

1.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Apptainer on HPC

Data formatted according to:

BIDS

2

Hi @Kai_Glahn and welcome to neurostars!

In the future, please try to provide as much information from the Software Support post template as possible. Notably you did not share your code.

I don’t think you are looking in the right place for the GQI outputs. They should be in $OUTPUT_DIR/derivatives/qsirecon-DSIStudio/sub-XX/dwi

Read more about expected outputs here: Built-In Reconstruction Workflows — qsirecon 1.0.2.dev5+gaf43da9 documentation

Best,
Steven

3

Hi @Steven thank you for your prompt response!

My apologies, I was sending in my question from my phone last night, but have updated my post to include code and question. Let me know if more information is needed to discover my issue.

Kindly,
Kai