Summary of what happened:
I ran the fmriprep command above with hopes that my analysis would run both in native space (T1w space with no normalization) plus, MNI normalization.
Also, I added a parameter to force skull stripping.
However, only the MNI-space image has been skullstripped, not the native T1w image.
I can see that the skull could be stripped cleanly using the brainmask, however, doesn’t the software automatically do this?
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep-docker /
Nifti /
derivatives /
--participant_label 125 /
--work-dir work /
--fs-license-file license.txt /
--output-spaces T1w MNI152NLin2009cAsym /
--n_cpus 12 --omp-nthreads 2 --mem-mb 16000 /
--fs-no-reconall /
--skip-bids-validation /
--skull-strip-t1w force
Version:
Latest (25.2.3 at this time)
Environment (Docker, Singularity / Apptainer, custom installation)
Docker
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