tkregister command failed in FreeSurferPipeline

[Lara]

Dear experts, 

I'm trying to run the HCP structural pipelines on a test subject and got through the PreSurferPipeline without problems, but am now struggling with an error related to the tkregister command in the FreeSurferPipeline. 

This is the error output I get:

HMSI/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Tue Jan 26 23:39:06 CET 2021:FreeSurferPipeline.sh: While running '/Volumes/HMSI/A/HCP_Test/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh --subject=Atest --subjectDIR=/Volumes/HMSI/A/HCP_Test/Atest/T1w --t1=/Volumes/HMSI/A/HCP_Test/Atest/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/Volumes/HMSI/A/HCP_Test/Atest/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/Volumes/HMSI/A/HCP_Test/Atest/T1w/T2w_acpc_dc_restore.nii.gz':

Tue Jan 26 23:39:06 CET 2021:FreeSurferPipeline.sh: ERROR: tkregister command failed with return_code: 1

From what I've gathered from an older post on the Freesurfer Mail archive this seems to be related to the fact that Mac Catalina doesn't support 32 bit binaries - I haven't been able to resolve the issue however. Does anyone here have any ideas on how I could go about this - ideally without having to revert back to an older Mac OS version?

I am v 4.2.0 of the pipelines with FSL v 6.0.4, FreeSurfer v 6.0.0, workbench v 1.4.2 on macOS Catalina v 10.15.7.

Best regards,

Lara

[Ogawa Akitoshi]

Hi Lara

You can use tkregister2_cmdl instead of tkregister2 on Catalina.

Please replace tkregister2 with tkregister2_cmdl in the scripts of FreeSurferPipeline and GenericfMRIVolumeProcessingPipeline.

You do not need to go back to an older version.

Best,

Akitoshi

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/bbfc644d-1d4f-48e6-9bf3-9c8bbbb93069n%40humanconnectome.org.

--

------------------------------------------------------------------

Akitoshi Ogawa, Ph.D.

Faculty of Medicine, Juntendo University

2-1-1 Hongo, Bunkyo City, Tokyo, 113-8421 Japan

TEL: +81-3-5802-1027

------------------------------------------------------------------

[Lara]

Hey Akitoshi,

thank you for the pointer- that seems to have worked! 

Best,

Lara