XCP-D uses the output of FMRIPREP to generate denoised BOLD images, parcellated time-series, functional connectivity matrices, and quality assesment reports.

References:

• Adebimpe, Azeez, Bertolero, Maxwell, Mehta, Kahini, Salo, Taylor, Murtha, Kristin, Cieslak, Matthew, Meisler, Steven, Madison, Thomas, Sydnor, Valerie, Covitz, Sydney, Fair, Damien, & Satterthwaite, Theodore. XCP-D : A Robust Postprocessing Pipeline of fMRI data. Zenodo. https://doi.org/10.5281/zenodo.7717239.

• XCP-D Documentation
• Github page

• Module Name: xcp_d (see the modules page for more information)
• Test data in $XCP_D_TEST_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load xcp_d
[+] Loading xcp_d  0.5.0  on cn3144 
[+] Loading singularity  3.10.5  on cn3144 

[user@cn3144 ~]$ xcp_d --help
usage: xcp_d [-h] [--version] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-t TASK_ID] [-m] [-s] [--nthreads NTHREADS] [--omp-nthreads OMP_NTHREADS]
[--mem_gb MEM_GB] [--use-plugin USE_PLUGIN] [-v] [--input-type {fmirprep,dcan,hpc}]
[--smoothing SMOOTHING] [--despike]
[-p {27P,36P,24P,acompcor,aroma,acompcor_gsr,aroma_gsr}]
[-c CUSTOM_CONF] [-d DUMMYTIME] [--lower-bpf LOWER_BPF] [--upper-bpf UPPER_BPF]
[--bpf-order BPF_ORDER] [--motion-filter-type {lp,notch}]
[--band-stop-min BAND_STOP_MIN] [--band-stop-max BAND_STOP_MAX]
[--motion-filter-order MOTION_FILTER_ORDER] [-r HEAD_RADIUS]
[-f FD_THRESH] [-w WORK_DIR] [--clean-workdir] [--resource-monitor] [--notrack]
fmri_dir output_dir

xcp_d postprocessing workflow of fMRI data

positional arguments:
  fmri_dir              the root folder of a preprocessed fMRI output .
  output_dir            the output path for xcp_d

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. xcp_d.sh). For example (using test data below):

#!/bin/bash
#SBATCH --job-name=xcp_d
#SBATCH --gres=lscratch:20
#SBATCH --mem=8g
#SBATCH --time=2:00:00
#SBATCH --cpus-per-task=4

module load xcp_d/0.5.0

tar -C /lscratch/${SLURM_JOB_ID} -xf ${XCP_D_TEST_DATA}/fmriprep.out.ds001.tar.gz

xcp_d /lscratch/${SLURM_JOB_ID}/fmriprep.out.ds001 /data/$USER/xcp_d.out\
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID}  

Submit this job using the Slurm sbatch command.

sbatch xcp_d.sh

Create a swarmfile (e.g. xcp_d.swarm). For example:

xcp_d /data/${USER}/BIDS-dataset/fmriprep.out.ds001/ /data/$USER/XCP-D/xcp_d.out.ds001 \
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID} \
xcp_d /data/${USER}/BIDS-dataset/fmriprep.out.ds002/ /data/$USER/XCP-D/xcp_d.out.ds002 \
         participant --participant_label sub-02 -w /lscratch/${SLURM_JOB_ID} \
xcp_d /data/${USER}/BIDS-dataset/fmriprep.out.ds003/ /data/$USER/XCP-D/xcp_d.out.ds003 \
         participant --participant_label sub-03 -w /lscratch/${SLURM_JOB_ID} \

Submit this job using the swarm command.

swarm -f xcp_d.swarm [--gres=lscratch:#] [-g #] -t auto --module xcp_d