Issue Running XCP-D (v0.10.7) in Volumetric Mode with --mode abcd

Software Support
1

Summary of what happened:

Dear XCP-D Team,

I hope this message finds you well. I’m reaching out regarding an issue I’ve encountered when trying to run XCP-D in volumetric format with NIfTI outputs.

Specifically, I would like to run XCP-D with --mode abcd, but it seems this mode does not generate the expected NIfTI outputs. The only configuration that has worked for me so far is setting --mode none and manually specifying additional flags, and I have to have both --file-format nifti and --warp-surfaces-native2std n.

Below is the full command I’m currently using. It runs successfully under ‘–mode none’, but only generates one QC report, within which some expected QC figures and text are missing.

Could you please advise:

  1. whether --mode abcd is compatible with volumetric nifti output?
  2. if not, is there a recommended configuration for running XCPD in volumetric mode using standardized pipeline like abcd?

I would really appreciate any guidance or clarification you can provide.

Kind regards,
Mahta

Command used (and if a helper script was used, a link to the helper script or the command generated):

apptainer run --cleanenv \
/data/sugrue1/ntrc/xcp_d_0.10.7.sif \
/fmriprep_path/derivatives/fmriprep \
/output_path \
participant \
--participant-label test04 \
--mode none \
--input-type fmriprep \
--file-format nifti \
--warp-surfaces-native2std n \
--combine-runs n \
--abcc-qc n \
--linc-qc n \
--output-type censored \
--min-coverage 0.6 \
--smoothing 6 \
--motion-filter-type notch \
--band-stop-min 12 \
--band-stop-max 18 \
--motion-filter-order 4 \
--fd-thresh 0.5 \
--despike y \
--nuisance-regressors 36P \
--lower-bpf 0.01 \
--upper-bpf 0.1 \
--bpf-order 2 \
--create-matrices all \
--dummy-scans 10 \
--fs-license-file /FS_path/freesurfer_license.txt \
--omp-nthreads 3 \
--nthreads 8 \
-w /Path_to_work_xcpd \
--verbose

Version:

0.10.7

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

Apptainer

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @mahta.karimpoor,

In the future, please use the Software Support post category and template, as well as tagging the appropriate software. You can see I edited in for you this time.

What happens when you manually override the --file-format in ABCD mode? If it still doesn’t work you can just create a modified version based on the ABCD mode defaults (Processing Pipeline Details — xcp_d 0.11.0rc2.dev35+gd3ee7d3 documentation)

[workflow]
mode = "abcd"
file_format = "cifti"
dummy_scans = 0
input_type = "fmriprep"
despike = true
smoothing = 6
output_interpolated = true
combine_runs = true
motion_filter_order = 4
head_radius = 50
fd_thresh = 0.3
min_time = 240
bandpass_filter = true
high_pass = 0.01
low_pass = 0.08
bpf_order = 2
min_coverage = 0.5
correlation_lengths = []
process_surfaces = true
abcc_qc = true
linc_qc = true

Best,
Steven

1 Like