On 25 Sep 2022, at 18:52, Douglas N. Greve <dgreve@MGH.HARVARD.EDU> wrote:

I've also attached a new mri_sclimbic_seg. You can copy it to $FREESURFER/python/scripts/mri_sclimbic_seg

On 9/23/2022 10:52 AM, Kumar, Avnish wrote:

Hi Markus,

This bug has been fixed in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the mri_sclimbic_seg/mri_sclimbic_seg file into the appropriate subfolder (<FS_install_dir>/python/scripts/mri_sclimbic_seg) where you installed FS or you could simply edit the mri_sclimbic_seg file at that location as in the bug fix.

Best,

Avnish

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Markus Handal Sneve <m.h.sneve@psykologi.uio.no>
Sent: Wednesday, September 21, 2022 5:17 PM
To: Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_sclimbic_seg: --conform not conforming?

 

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Hi,

I’m testing mri_sclimbic_seg in the new FS version (7.3.2). My structurals are 0.8mm isotropic, so I’m adding the —conform flag, but still get this error:

<PastedGraphic-2.png>

Any ideas?

And, BTW, I had to set the environmental variable HDF_USE_FILE_LOCKING to FALSE to get the tool running. Perhaps a tip to add to the wiki, if not people can now see it here.

Thanks for your great work!

Cheers,

Markus

Markus Handal Sneve, Ph.D.
Center for Lifespan Changes in Brain and Cognition
Department of Psychology 
University of Oslo

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