I have tried using singularity in a HPC. Everything runs good without errors or some error mesages. The folders are correctly created, the images are created, the html report is created. But when I open the html report file, the links for the imagens are not there. The html file only contains link “Methods” (HTML, Markdown, Latex) and “Errors”( No errors report!). The links “Summary”, “Anatomical”, “Functional Reports for:” and “About” are not created. Any suggestion?
Thanks in advance
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv -B /home/bpastorello/project:/home/bpastorello/project -B /opt/freesurfer/license.txt:/opt/freesurfer/license.txt /opt/singularity/fmriprep-23.1.4.simg /home/bpastorello/project/root_bids /home/bpastorello/project/fmriprep/sub-01 participant --participant-label sub-01 --skip-bids-validation --fs-no-reconall --stop-on-first-crash --fs-license-file /opt/freesurfer/license.txt
231023-10:51:22,529 nipype.workflow INFO:
[Node] Executing “apply_mask” <niworkflows.interfaces.nibabel.ApplyMask>
231023-10:51:22,628 nipype.workflow INFO:
[Node] Finished “apply_mask”, elapsed time 0.096849s.
231023-10:51:26,416 nipype.workflow IMPORTANT:
fMRIPrep finished successfully!
231023-10:51:26,432 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
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