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 < ayend...@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 >> <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 >> >> >> >> >> >> >> >> 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<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. >> >> >> >>
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