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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Thanks a lot Nick
Actually a I have already downloaded the file yesterday, but it gives another error in the same step when i re-run the recon-all autorecon2, says the version of the centos and FS, later say "bus error" but continue the recon till it gets to the Subcortical segmentation, where this massage appears again, any idea of what could be the problem?
#@# SubCort Seg Tue Jun 1 00:36:42 CEST 2010
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
Bus error
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 Tue Jun 1 00:36:42 CEST 2010
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Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea???
#@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010
/root/trabajo/freesurfer/subjects/T1_GE1/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: aseg volume aseg.mgz must be conformed
using MR volume brainmask.mgz to mask input volume...
unconformed source detected - conforming...
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 Wed Jun 2 14:59:06 CEST 2010
Best, Gabriel _________________________________________________________________ ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html
Hi Gabriel,
did you do anything "nonstandard" to your aseg volume or anywhere else in the stream? The aseg should be 256^3 1imm iso, but for some reason it's not.
Bruce On Wed, 2 Jun 2010, Gabriel Go.Es. wrote:
Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea???
#@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010
/root/trabajo/freesurfer/subjects/T1_GE1/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: aseg volume aseg.mgz must be conformed
using MR volume brainmask.mgz to mask input volume...
unconformed source detected - conforming...
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 Wed Jun 2 14:59:06 CEST 2010
Best, Gabriel
¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html
Bruce, No i did not, but the acquisition was made with a voxel of 0.8^3mm, that's why i put the -cm flag to the autorecon1, but i didn't made any other change, is there any way to normalize the size of the image, without recon?
Thanks, Gabriel
Date: Wed, 2 Jun 2010 15:12:21 -0400 From: fischl@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: nicks@nmr.mgh.harvard.edu; reuter@mit.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] autorecon2 error
Hi Gabriel,
did you do anything "nonstandard" to your aseg volume or anywhere else in the stream? The aseg should be 256^3 1imm iso, but for some reason it's not.
Bruce On Wed, 2 Jun 2010, Gabriel Go.Es. wrote:
Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea???
#@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010
/root/trabajo/freesurfer/subjects/T1_GE1/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: aseg volume aseg.mgz must be conformed
using MR volume brainmask.mgz to mask input volume...
unconformed source detected - conforming...
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 Wed Jun 2 14:59:06 CEST 2010
Best, Gabriel
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_________________________________________________________________ ¿Quieres descubrir todos los trucos de Windows 7? ¡Hazlo aquí! http://www.sietesunpueblodeexpertos.com/index_windows7.html
Hi Gabriel,
that's probably what's causing the problems. Unfortunately a bunch of us are off to HBM, so it may be a little while before we get to fix it.
Bruce On Wed, 2 Jun 2010, Gabriel Go.Es. wrote:
Bruce, No i did not, but the acquisition was made with a voxel of 0.8^3mm, that's why i put the -cm flag to the autorecon1, but i didn't made any other change, is there any way to normalize the size of the image, without recon?
Thanks, Gabriel
Date: Wed, 2 Jun 2010 15:12:21 -0400 From: fischl@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: nicks@nmr.mgh.harvard.edu; reuter@mit.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] autorecon2 error
Hi Gabriel,
did you do anything "nonstandard" to your aseg volume or anywhere else in the stream? The aseg should be 256^3 1imm iso, but for some reason it's not.
Bruce On Wed, 2 Jun 2010, Gabriel Go.Es. wrote:
Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea???
#@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010
/root/trabajo/freesurfer/subjects/T1_GE1/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: aseg volume aseg.mgz must be conformed
using MR volume brainmask.mgz to mask input volume...
unconformed source detected - conforming...
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 Wed Jun 2 14:59:06 CEST 2010
Best, Gabriel
¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
¿Quieres descubrir todos los trucos de Windows 7? ¡Hazlo aquí! http://www.sietesunpueblodeexpertos.com/index_windows7.html
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gabriel Go.Es. -
Nick Schmansky