mri_ca_label can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
copy it your $FREESURFER_HOME/bin
n.
On Mon, 2010-05-31 at 03:25 -0400, Martin Reuter wrote:
Yes, looks like the one I fixed. Nick can point you to a download for the fixed files.
Best, Martin
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Gabriel Go.Es." gabriellbk@hotmail.com Cc: "free surfer" freesurfer@nmr.mgh.harvard.edu; "Reuter, Martin -- Martin Reuter" mreuter@nmr.mgh.harvard.edu; "Martin Reuter" reuter@mit.edu Sent: Sunday, May 30, 2010 4:50 PM Subject: Re: [Freesurfer] autorecon2 error
Hi Gabriel,
I think Martin fixed this bug, didn't you Martin?
Bruce
On Sun, 30 May 2010, Gabriel Go.Es. wrote:
Dear FreeSurfers I run an autorecon1 using the flag -no-wsgcaatlas for skullstripping, I'm using freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached the recon-all_status log for any information you may need Then I was trying to run the autorecon2: recon-all -subjid -autorecon2 when it gives the following error message:
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $
/root/trabajo/freesurfer/bin/recon-all
PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri
CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 1.05 x + 0 estimating mean gm scale to be 1.16 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.43 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010
any suggestions and help will be so appreciated
Best
Gabriel
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