Thanks Anastasia. Your suggestion worked. On Wed, Feb 25, 2015 at 4:10 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote:
> > Hi Alan - It can't find the file. Check the error message, part of the > path to the file is repeated twice. I suspect you typed that part in both > dcmroot and dcmlist. > > a.y > > > On Wed, 25 Feb 2015, Alan Francis wrote: > > Hi Anastasia: >> I have run trac-all using the following command: >> >> trac-all -prep -c /data/alanf/FreeSurfer_5.3/ >> diffusion_recons/dmrirc-101309 >> >> However, I get an error message which is as follows: >> >> INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons >> >> INFO: Diffusion root is /data/alanf/FreeSurfer_5.3/diffusion_recons/ >> >> Actual FREESURFER_HOME /cm/shared/freesurfer >> >> trac-preproc -c >> /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/dmrirc.local >> -log >> /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/trac-all.log >> -cmd /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/ >> scripts/trac-all.cmd >> >> #------------------------------------- >> >> /cm/shared/freesurfer/bin/trac-preproc >> >> #------------------------------------- >> >> #@# Image corrections Wed Feb 25 11:52:55 EST 2015 >> >> mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/ >> FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz >> /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz >> >> mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/ >> FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz >> /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz >> >> niiRead(): error opening file /data/alanf/FreeSurfer_5.3/ >> diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_ >> recons/101309/Diffusion/data.nii.gz >> >> $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ >> >> reading from /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/ >> FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz... >> >> crypt_gkey = *CbLO7a8FzSPM >> >> Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 >> x86_64 x86_64 x86_64 GNU/Linux >> >> >> trac-preproc exited with ERRORS at Wed Feb 25 11:52:55 EST 2015 >> >> >> Should I convert the nii.gz file to nii? I enclose the configuration file >> for your perusal. >> >> >> thank you so much, >> >> >> best, >> >> >> Alan >> >> >> -- >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> >> Alan N. Francis PhD >> NIDA T32 Fellow in Drug Abuse & Brain Imaging >> Brain Imaging Center >> McLean Hospital >> Harvard Medical School >> 115 Mill Street, Belmont, MA 02478 >> al...@bwh.harvard.edu >> afran...@mclean.harvard.edu >> >> >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> >> >> > > 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. > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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