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Dear Freesurfer team,

I am attempting to use freesurfer using fmriprep but I get the following error message:

error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed

I've searched the archive but couldn't find a solution. Does anyone have any thoughts on how to trouble-shoot this one?

I've contacted you before and was asked to look at the input to that step -

It seems like the problem is indeed somewhere else in the process, if I understand correctly, at "autorecon1"

[Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function> 240417-14:16:30,667 nipype.workflow INFO: [Node] Finished "fs_isrunning", elapsed time 0.004s. 240417-14:16:44,30 nipype.workflow INFO: [Node] Setting-up "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" in "/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1". 240417-14:16:44,70 nipype.workflow INFO: [Node] Executing "autorecon1" <smriprep.interfaces.freesurfer.ReconAll> 240417-14:16:44,77 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:44,78 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:52,329 nipype.workflow INFO: [Node] Finished "autorecon1", elapsed time 8.257549s. 240417-14:16:52,337 nipype.workflow WARNING: [Node] Error on "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" (/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1) 240417-14:16:52,558 nipype.workflow ERROR: Node autorecon1 failed to run on host benyakov-a.elsc.huji.ac.il. 240417-14:16:52,569 nipype.workflow ERROR: Saving crash info to /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sub-01/log/20240417-141555_c3b0815f-caf3-41ba-ab5a-fb57155be490/crash-20240417-141652-shahar.bennoun-autorecon1-682b0086-8863-4f60-9204-6d485fe4a790.txt

Also, I've been asked to post "a couple of images of the processing (the orig.mgz, the T1.mgz, the brainmask.mgz, …)", what does that mean? How do I do it?

1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 2) Platform: Linux 3) PlatformVersion: 5.4.0-159-generic

#176-Ubuntu SMP Mon Aug 14 12:04:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 16 13:13:35 IDT 2024

4) recon-all.log 5) autorecon1 command

Best regards, Shahar