Xcp-d output on surface

Software Support
,
1

I have trouble getting xcp-d output in fsLR space. I wonder if anyone had any thoughts.

I run fMRIprep:

singularity run -B $HOME/.cache/templateflow:/opt/templateflow,$bids_root_dir:/mnt /home/test-oc/singularity/images/fmriprep-23.0.2.simg \
	    /mnt/rawdata/ $deriv  \
	    participant \
	    --participant-label ${subject} \
	    -w $work \
	    --fs-license-file /mnt/tbsfdg/scripts/license.txt \
	    --fs-subjects-dir /mnt/${SD} \
	    --output-spaces MNI152NLin6Asym:res-2 fsaverage:res-native \
	    --use-aroma \
	    --write-graph \
	    --nthreads $nthreads \
	    --omp-nthreads $nthreads \
	    --bids-filter-file $filter \
	    --verbose &

After which I get an output in the derivatives called:
“sub-tbsfdg006_ses-002_task-rest_run-03_hemi-L_space-fsaverage_bold.func.gii”

I then run xcp-d in the hopes that I would get the data in fslr

singularity -d run -B $HOME/.cache/templateflow:/opt/templateflow,/group/tuominen/TBS-FDG:/mnt \
/home/lauri/Documents/xcp_d-0.6.0.simg \
/mnt/derivatives/iter6s2 /mnt/xcp-d_output_s2/ participant \
--combineruns --nuisance-regressors 36P \
--min-coverage 0.5 \
--min-time 100 --dummy-scans 0 --bpf-order 2 --lower-bpf 0.01 --upper-bpf 0.08 \
--head-radius auto --fd-thresh 0.3 --warp-surfaces-native2std --cifti \
--nthreads 54 --omp-nthreads 3 -v

But this gives me the following error:

240919-14:29:27,875 nipype.workflow INFO:
Beginning the xcpd_wf workflow
Process Process-2:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.8/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.8/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/cli/run.py”, line 977, in build_workflow
retval[“workflow”] = init_xcpd_wf(
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflows/base.py”, line 199, in init_xcpd_wf
single_subj_wf = init_subject_wf(
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflows/base.py”, line 370, in init_subject_wf
layout, subj_data = collect_data(
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/utils/bids.py”, line 276, in collect_data
raise FileNotFoundError(
FileNotFoundError: No BOLD data found in allowed spaces (fsLR).

Without the --warp-surfaces-native2std --cifti -flags everything runs nicely.

Version:

xcp_d-0.6.0.simg
fmriprep-23.0.2.simg

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

singularity

2

Hi @lauri,

XCP_D does not currently support fsaverage or fsnative surfaces (which are in GIFTI, not CIFTI, format). fsLR is the result of the --cifti-output workflow, which it does not seem like you did for fMRIPrep.

I also in general recommend updating XCP_D as 0.6.0 is fairly out of date.

Best,
Steven

3

Oh! amazing thanks for the quick reply! I will rerun fMRIprep and update my xcp-d. Cheers
Lauri

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