Summary of what happened:
I have preprocessed both structural (T1w and T2w) and functional (BOLD) data of a single subject using fMRIPrep and specifying T2w as one of the output spaces, but after completing the preprocessing no outputs related to T2w seem to be present whatsoever. I reckon to have read that disabling freesurfer reconstruction may be the cause, but I am not sure.
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep \
../dataset/raw \
../dataset/derivatives \
participant \
--derivatives ../dataset/derivatives \
--participant-label OAS30001 \
--skip-bids-validation \
--n-cpus 6 \
--omp-nthreads 8 \
--mem-mb 14000 \
--output-spaces T2w MNI152NLin2009cAsym:res-2 \
--bold2anat-init t2w \
--random-seed 34 \
--fs-license-file ../freesurfer/license.txt \
--fs-no-reconall \
--work-dir /tmp/fmriprep_works/OAS30001 \
--notrack
Version:
fmriprep 25.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
NeuroDesktop
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
Screenshots / relevant information:
I attach a screenshot of the anatomical outputs:
