Hello FreeSurfer Developers,

 

I am trying to run the hippocampal and amygdala subfield segmentation and take advantage of the .6mm resolution of the scan.  I was able to run recon-all successfully on the scan without the -cm option. 

 

I get the following error:

 

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

SUBJECT nomove_xpace_06mm_tr3bcm

DATE Fri Aug  3 11:58:33 EDT 2018

USER flalonde

HOST cn0638

PROCESSOR x86_64

OS Linux

Linux cn0638 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $

/data/flalonde/freesurfer_dev/bin/recon-all

PWD /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/scripts

CMD mris_register -curv -rusage /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /data/flalonde/freesurfer_dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg

 

I’ve attached a copy of the recon-all.log

 

1)  Freesurfer version:  freesurfer-linux-centos7_x86_64-dev-20180723-7bf4760

2)  Platform:  CentOS Linux release 7.5.1804 (Core)

3)  uname -a:  Linux felix.nimh.nih.gov 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4)  recon-all.log:  see attached

 

 

The list mentions running a post-hoc surface deformation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47309.html) using mris_make_surfaces as a workaround but I’m not sure if this is applies in my case or what the full command might be (e.g. mris_make_surfaces subjectname lh).

 

Thanks,

 

François M. Lalonde, Ph.D.

DNU / HGB / DIRP / NIMH

10 Center Drive, Room 4N244

Bethesda, MD  20892-1600