I tried to run fmriprep with and without the lesion included in my “anat” directory labeled as “sub-01_T1w_label-lesion_roi.nii.gz”. I used the same command for both, and when I run it excluding the lesion, all of the output files are in the correct place, and I get a sub-01 html output as well, but when I include the lesion file, I only get the following outputs:
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
And here are the last few lines out the log (with the lesion):
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_AO_run_03_wf.bold_reg_wf.bbreg_wf.bbregister".
180807-00:42:15,244 nipype.workflow INFO:
[Node] Finished "_midthickness1".
180807-00:42:21,882 nipype.workflow INFO:
[Node] Finished "_midthickness0".
Should I not be running the same command when including a lesion file? I was under the impression that it would include the lesion mask for registration as long as the lesion was in BIDS compatible format…