fMRIPrep fails on 1 subject amongst 3 in my dataset (T1w) - Node Name: fmriprep_25_0_wf.sub_02_wf.anat_fit_wf.surface_recon_wf.autorecon1

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Thank you @Steven for your answer.

It looks like the -cw256 flag is by default applied by fMRIprep. In my case, it is correctly applied:

Cmdline:
	recon-all -autorecon1 -i /tmp/work/fmriprep_25_0_wf/sub_02_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-02_T1w_noise_corrected.nii.gz -noskullstrip -noT2pial -noFLAIRpial -cw256 -hires -openmp 8 -subjid sub-02 -sd /out/sourcedata/freesurfer -expert /tmp/work/fmriprep_25_0_wf/sub_02_wf/anat_fit_wf/surface_recon_wf/autorecon1/expert.opts
Stdout:
	INFO: hi-res volumes are conformed to the min voxel size
	fs-check-version --s sub-02 --o /tmp/tmp.VEilH3
	Mon Mar 31 12:59:24 UTC 2025

	setenv SUBJECTS_DIR /out/sourcedata/freesurfer
	cd /tmp/work/fmriprep_25_0_wf/sub_02_wf/anat_fit_wf/surface_recon_wf/autorecon1
	/opt/freesurfer/bin/fs-check-version --s sub-02 --o /tmp/tmp.VEilH3
	-rwxrwxr-x 1 root root 18565 Aug  4  2022 /opt/freesurfer/bin/fs-check-version

	freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	$Id$
	Linux 5d965cd3d4b8 5.15.0-134-generic #145~20.04.1-Ubuntu SMP Mon Feb 17 13:27:16 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
	pid 1027
	Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	Subject does not have a bstampfile, copying /opt/freesurfer/build-stamp.txt
	Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	No constraints on version because REQ=UnSet and FsVerFile=NotThere
	#@#% fs-check-version match = 1
	fs-check-version Done
	INFO: SUBJECTS_DIR is /out/sourcedata/freesurfer
	Actual FREESURFER_HOME /opt/freesurfer
	Linux 5d965cd3d4b8 5.15.0-134-generic #145~20.04.1-Ubuntu SMP Mon Feb 17 13:27:16 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
	-cw256 option is now persistent (remove with -clean-cw256)
	/out/sourcedata/freesurfer/sub-02

According to this answer, there may be a conflict between -cw256 and -hires.
It is then advised in this answer to crop the images with tools such as fslroi, so they are conform to 256x256x256 1mm isotropic.

In my case, MRIcroGL says my T1w.nii.gz (bids\sub-XX\anat\sub-XX_T1w.nii.gz) and my orig.mgz (fmriprep\sourcedata\freesurfer\sub-XX\mri\orig.mgz) are

  • sub-02 : T1w (104 x 121 x 155) = 2734 // orig (160 x 132 x 156) = 179
  • sub-03 : T1w (104 x 132 x 171) = 2934 // orig (159 x 142 x 170) = 240
  • sub-04 : T1w (104 x 125 x 170) = 2678 // orig (159 x 135 x 169) = 192

which makes me doubt about the ERROR! FOV=258.400 > 256 issue, because I see no particular size issue in sub-02. Maybe I am not refering to the correct values in MRIcroGL.

All in, how to correct the specific FOV issue for that subject?
Also, how can I optimise the FOV prescription in my protocol, so this doesn’t occur again in the future?

Thank you.