Hi Alan - The file doesn't need to have an extension, .txt or other. But
you do need to set bvecfile to the full name of the file, including the
extension, if it has one.
a.y
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.
thanks,
Alan
On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons/bvecs.txt': No such file or directory
Does this file exist?
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi All:
When I ran trac-preproc I got an error that read s as
follows:
trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT
2013. I do have a bvec.txt and bval file in each
directory.
thanks for your help,
Alan
The following are the messages:
csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/dmrirc
INFO: SUBJECTS_DIR
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs
INFO: Diffusion root
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
Actual FREESURFER_HOME
/autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc
-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/scripts/dmrirc.local -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/scripts/trac-all.log -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Aug 5 13:12:10 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValera
s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/dmri/dwi_orig.nii.gz
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValera
s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValera
s012a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989696, 0.0161603, 0.142271)
j_ras = (0.0163, 0.999867, -0.000183368)
k_ras = (0.142255, -0.00213754, 0.989828)
writing
to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/dmri/dwi_orig.nii.gz...
cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/dmri/dwi_orig.mghdti.bvecs
cp: cannot
stat`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons/bvecs.txt': No such file or directory
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT
2013
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