Fmriprep error - mritotal: Command not found

Summary of what happened:

Dear Community,

I have successfully run fmriprep for most of my participants. However, two participants show the same error. I wonder what the issue is here. Can anyone kindly tell me what was wrong please?
Thank you

Command used (and if a helper script was used, a link to the helper script or the command generated):



Environment (Docker, Singularity / Apptainer, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:


Relevant log outputs (up to 20 lines):

This is the error in the log:

Fri Feb  9 08:10:20 GMT 2024
	tmpdir is transforms/tmp.talairach.3928214
	mri_convert orig_nu.mgz transforms/tmp.talairach.3928214/src.mnc
	mri_convert orig_nu.mgz transforms/tmp.talairach.3928214/src.mnc 
	reading from orig_nu.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, -5.82077e-10, -1.86265e-09)
	j_ras = (0, 3.72529e-09, -1)
	k_ras = (-5.82077e-10, 1, 0)
	writing to transforms/tmp.talairach.3928214/src.mnc...
	mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3928214/src.mnc transforms/
	mritotal: Command not found.
	ERROR: mritotal failed, see transforms/talairach.log
	Linux 4.18.0-513.11.1.el8_9.x86_64 #1 SMP Wed Jan 17 02:00:40 EST 2024 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s sub-274 exited with ERRORS at Fri Feb  9 08:10:22 GMT 2024

	For more details, see the log file /data/project/CannTeen/CannTeen_longitudinal_fMRI/SST_11/output/sub-274/sourcedata/freesurfer/sub-274/scripts/recon-all.log
	To report a problem, see


	RuntimeError: subprocess exited with code 1.

240209-08:10:25,230 cli ERROR:
	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: 274 (1). Check the HTML reports for details.
240209-08:10:26,251 nipype.workflow INFO:
	 [Node] Finished "07_fill_gm", elapsed time 19.691168s.

Screenshots / relevant information:

Hi @wang_simiao, and welcome to neurostars!

In the future, please submit software related posts under the Software Support category, which prompts you to give us important information for debugging your problem. I have edited your post to reflect the post template, but you can see there’s still important info missing. You can edit your post to add this information in.

Although you did not report your version, I am guessing it is not 23.2.0, since this error was addressed in a software update (see `mritotal` subcommands not found · Issue #3103 · nipreps/fmriprep · GitHub). So unless you are already using 23.2.0, please update and try again.