Summary of what happened:
Hi everyone,
I’m using XCP-D on fMRIprep output. Looking at the executive summary of my subjects, I see that the first images from “BrainSprite Viewer: T1” show misaligned surfaces with respect to the anatomical data:
I’m not sure what thes surfaces actually are.
In the same XCP-D summary report, the alignment between the atlas and the T1w images also looks fine:
Any help in sorting this out would be greatly appreciated!
Best wishes,
Roey
Command used:
The command includes several environment variables, which I left as is for readability.
apptainer run --cleanenv --bind $FMRI_PATH,$LAB_SHARED "${XCPD_IMG}" \
${FMRI_PATH}derivatives_${SUBJECT} \
${FMRI_PATH}/derivatives/xcp_d_070_acompcor_withtedana \
participant \
-w ${FMRI_PATH}/derivatives/xcpd_work \
--participant_label "${SUBJECT}" \
--nuisance-regressors "${REGRESSORS}" \
--fs-license-file="${FREESURFER_LICENSE}" \
--custom_confounds ${FMRI_PATH}/derivatives/custom_confounds_for_xcpd_ortho \
--bids-filter-file "${LAB_SHARED}/CFG/code/Automated_Pipeline/functional_pipeline/xcpd_bids_filter.json" \
--cifti
Version:
0.7.0 (a little outdated, I know)
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity image running via Apptainer.
Data formatted according to a validatable standard? Please provide the output of the validator:
Data is in BIDS standard, but sue to possible misformatted directories, I decided to skip BIDS validation.
Relevant log outputs (up to 20 lines):
N/A
Screenshots / relevant information:
When I load the subject’s FreeSurfer output in freeview, the pial and white-matter surfaces look perfectly fine, suggesting that it’s not an issue of FreeSurfer’s surfaces:
Note that I’m using an older version of XCP-D since I followed this example for using custom confounds. Newer versions of XCP-D use a different syntax for that.