Re: [Freesurfer] problem with trac-all -prep proc stage - Freesurfer

26 Feb 2013

      Make sure doregcvs is not set to 1 in your config file. This option is not 
meant to be used in 5.1 but will be in 5.2.
On Tue, 26 Feb 2013, Jon Wieser wrote:
...
hi anastasia,
i don't know what "CVS for inter-subject registration " is.
Jon
----- Original Message -----
From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu
To: "Jon Wieser" wieser@uwm.edu
Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, February 26, 2013 1:32:34 PM
Subject: Re: [Freesurfer] problem with trac-all  -prep  proc stage
Hi Jon - Are you trying to use CVS for inter-subject registration?
a.y
On Tue, 26 Feb 2013, Jon Wieser wrote:
...
hello
i ran a trac-all -prep -c ./dmrirc_single_subject   and got the following error:
flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.flt.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat
ln -sfn /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/cvs/cvs_avg35 /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs
mri_cvs_register --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs
Log file is freesurfer_to_cvs_avg35.mri_cvs_register.1302261152.log
Tue Feb 26 11:52:22 CST 2013
--mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs
$Id: mri_cvs_register,v 1.4.2.2 2010/08/11 17:52:00 nicks Exp $
cerebrum.uits.uwm.edu
Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
The outdir:
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs
mris_resample --atlas_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/cvs_avg35/surf/lh.sphere --annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/label/lh.aparc.annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.aparc.annot --subject_surf /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.white --subject_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.cvs.tocvs_avg35.sphere.reg --out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.white
Exception caught while parsing cmd-line
ambiguous option annot
Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Feb 26 11:52:22 CST 2013
Jon

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.