tkregister error while running FreeSurferPipeline.sh

[amirhussein.a]

Dear all,

I've done everything required (all installations) to run HCP structural analysis pipeline (v 4.3) on the data I have acquired (0.8 mm isotropic voxel-size T1/T2). The PreFreeSurfer ran smoothly (no gradient distortion correction), however, when I ran the FreeSurferPipelineBatch.sh it gave me an error after a few hours: tkregister command not found. I have installed the latest FreeSurfer v7. I remember I encountered the same error while running this command using the prior version of the HCP pipeline and it is quite interesting it hasn't been changed.

I edited the ${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh and replaced tkregister with tkregister2 (not "tkregister_cmd"s; attached). Rerunning the FreeSurferPipelineBatch.sh stopped instantly by giving an error in running recon-all, which I presume is due to the prior incomplete analysis. I couldn't find the "IsRunning" file to delete or do not know how to edit the FreeSurferPipeline.sh to continue recon-all where it has stopped.

Any comments are appreciated.

Bests,

Amir

[Glasser, Matthew]

This isn’t fixed because we don’t recommend using FreeSurfer 7.X at this time.  It has worse placement of the cortical surfaces.   I would stick with FreeSurfer 6.X.

Matt.

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[chou keiyn]

Dear Amir and all,

I've done everything the same as you,and it occcured to me the same problem,that is,"tkregister command not found".When I replace it with "tkregister2",it gave me another error " MRISread(../surf/lh.white.preaparc.rawavg): could not open file".Is the reason that I used FreeSurfer 7.4?

Any comments are appreciated.

Bests,

Keiyn Chou

[Glasser, Matt]

We don’t currently support FreeSurfer 7.X due to regressions in surface quality.

 

Matt.

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[Dierker, Donna]

Specifically, the non-uniformity correction (ANTS4?) in Freesurfer 7 often misbehaves in Freesurfer 7.

I know multiple labs at WashU who have noticed this, one of which changed their configuration file to call ANTS3 rather than ANTS4.

Obviously this affects the surfaces.

If you use Freesurfer 7, be on the lookout for this.

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From: 'Glasser, Matt' via HCP-Users <hcp-...@humanconnectome.org>
Sent: Thursday, January 11, 2024 8:06 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Cc: amirhussein.a <amirhu...@gmail.com>
Subject: Re: [hcp-users] Re: tkregister error while running FreeSurferPipeline.sh

 

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[Glasser, Matt]

The issue is larger than that.  Basically, the surface placement is not very good.  We have worked with the FreeSurfer group and made some improvements, but not yet gotten FS 7.X up to FS 6 quality.

 

Matt.

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