Dear freesurfer experts:
Recon-all is running in a few seconds (obvious error).
I am getting the following screen output on Linux, when I run recon-all:
recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene -force INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 lab root 59398 May 13 15:07 /usr/local/freesurfer/subjects/arlene/scripts/recon-all.log Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/arlene
mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998356, -0.0445698, 0.0360538) j_ras = (0.0395912, -0.0812138, 0.99591) k_ras = (0.0414595, -0.9957, -0.0828448) writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz...
#------------------------------------------
recon-all finished without error at Thu May 13 15:08:08 BST 2010
The TR, flig angle etc. are all 0.00 ... Do you have any ideas?
Many thanks, Jason.
Hi Jason,
you have to tell it do do something (e.g. -autorecon2, -all, etc...)
cheers Bruce
On Thu, 13 May 2010, Jason Connolly wrote:
Dear freesurfer experts:
Recon-all is running in a few seconds (obvious error).
I am getting the following screen output on Linux, when I run recon-all:
recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene -force INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 lab root 59398 May 13 15:07 /usr/local/freesurfer/subjects/arlene/scripts/recon-all.log Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/arlene
mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998356, -0.0445698, 0.0360538) j_ras = (0.0395912, -0.0812138, 0.99591) k_ras = (0.0414595, -0.9957, -0.0828448) writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz...
#------------------------------------------
recon-all finished without error at Thu May 13 15:08:08 BST 2010
The TR, flig angle etc. are all 0.00 ... Do you have any ideas?
Many thanks, Jason.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks. It's working now. J
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 13 May 2010 15:12 To: Jason Connolly Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] freesurfer recon-all running in a few seconds without error?
Hi Jason,
you have to tell it do do something (e.g. -autorecon2, -all, etc...)
cheers Bruce
On Thu, 13 May 2010, Jason Connolly wrote:
Dear freesurfer experts:
Recon-all is running in a few seconds (obvious error).
I am getting the following screen output on Linux, when I run recon-
all:
recon-all -i
/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene - force
INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force
specified.
Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 lab root 59398 May 13 15:07
/usr/local/freesurfer/subjects/arlene/scripts/recon-all.log
Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52
EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/arlene
mri_convert
/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz
mri_convert
/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from
/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998356, -0.0445698, 0.0360538) j_ras = (0.0395912, -0.0812138, 0.99591) k_ras = (0.0414595, -0.9957, -0.0828448) writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz...
#------------------------------------------
recon-all finished without error at Thu May 13 15:08:08 BST 2010
The TR, flig angle etc. are all 0.00 ... Do you have any ideas?
Many thanks, Jason.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jason Connolly