I am output data using MNI152T1NLin6Asym:res-2 and T1w. My T1w images are 256x256x168 and bold is 64x64x41. When I view the output space-T1w_desc-preproc_bold.nii.gz, the images are even lower than the input bold: 40x47x41. Why is the space-T1w image not in the proper dimensions?
Summary of what happened:
I have ran fmriprep v24.1.1 on a 2 session dataset. Each session has 1 T1w and 1 fMRI. The T1w images are already brain extracted so I set --skull-strip-t1w to skip and output spaces as MNI152NLin6Asym:res-2 and T1w. The anat report looks just fine (brain mask/tissue segmentation, MNI registration shows 2mm resolution, reconall). However, when I view the alignment of the functionals to the T1w, the T1w is a lower resolution than the native func space (native func is 64x64x51 while the resulting resolution is 40x40x41):
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep-docker \
rawdata \
derivatives \
--participant-label 1101 \
--skip_bids_validation \
--write-graph \
--no-tty \
--nprocs 4 \
--mem-mb 16384 \
--bids-filter-file rawdata/bids_filter.json \
--output-spaces MNI152NLin6Asym:res-2 T1w \
--skull-strip-t1w skip \
--fs-license-file .license \
-w fmriprep_work
Version:
v24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
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):
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