You're welcome. It seems like it can't find this file:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train
I can't tell exactly what's going on without looking at your trac-all.log in its entirety. Can you please send it?
On Tue, 6 Aug 2013, Alan Francis wrote:
Thank you. It worked. I have been running a few brains and they have been preprocessed successfully. One brain gave me
an error message. Can you please help me address this:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/mni2diff.bbr.mat
--ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train: Command not found.
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 Tue Aug 6 10:22:18 EDT 2013
Thanks so much,
Alan
On Mon, Aug 5, 2013 at 3:55 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
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
<ayendiki@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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