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_recons/dmrirc INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ 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_recons//BW_101/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.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_recons//BW_101/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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
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_recons/dmrirc INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ 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_recons//BW_101/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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_recons//BW_101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.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_recons//BW_101/dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//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
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_recons/dmrirc INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/** BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons INFO: Diffusion root is /autofs/space/dali_003/users/** BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/ 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_recons//BW_101/**scripts/dmrirc.local -log /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons//BW_101/**scripts/trac-all.log -cmd /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons//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_recons//BW_101/**Diffusion_Recons/20080424_** 182054563000-000012-**000001DTIValeras012a001.nii /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons//BW_101/**dmri/dwi_orig.nii.gz mri_convert /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_ **Data/diffusion_recons//BW_101/**Diffusion_Recons/20080424_** 182054563000-000012-**000001DTIValeras012a001.nii /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons//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_recons//BW_101/**Diffusion_Recons/20080424_** 182054563000-000012-**000001DTIValeras012a001.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_recons//BW_101/**dmri/dwi_orig.nii.gz... cp /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons/bvecs.**txt /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** Data/diffusion_recons//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
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/**compliancelinehttp://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.
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 2013The 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.
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 2013The 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/**compliancelinehttp://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.
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 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.
Hi Anastasia:
The problem is solved. thanks so much,
Alan
On Tue, Aug 6, 2013 at 11:21 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
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 orother. 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 The information in this e-mail is intended only for the person towhom 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/**compliancelinehttp://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.
freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
Anastasia Yendiki