thanks. On Fri, June 13, 2014 12:30 pm, Anastasia Yendiki wrote: > > The right one to source is /usr/local/freesurfer/nmr-dev-env > > > On Fri, 13 Jun 2014, Shantanu Ghosh wrote: > >> Hi Anastasia, >> >> Thanks for the reply. >> >> After I edit my .tcshrc file to source the dev, I still get an error >> message. >> >> glia:shantanu[64] mynmr53 >> >> MNE software location set to: /usr/pubsw/packages/mne/stable >> MATLAB software not available >> >> /usr/pubsw/packages/mne/stable/bin added to PATH >> /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH >> /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to >> XUSERFILESEARCHPATH >> >> Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables >> correctly. >> Note: FreeSurfer environment is needed to access tkmedit from >> mne_analyze. >> >> glia:shantanu[65] fslview >> fslview: Command not found. >> >> >> >> Can you tell me if this is the right one to source? >> /autofs/cluster/freesurfer/centos6_x86_64/dev >> >> Or do I have to make further changes to my .tcshrc to access the dev >> version? >> >> Thanks in advance. >> Shantanu >> >> >> On Fri, June 13, 2014 12:02 pm, Anastasia Yendiki wrote: >>> >>> Hi Shantanu - The -qa flag was added in the update to tracula that was >> posted after the 5.3 release. >>> http://freesurfer.net/fswiki/Tracula/#Updates >>> >>> Martinos Center users can simply switch to the dev version of >>> freesurfer >> to take advantage of these updates, in which case you don't need to >> download anything. >>> >>> a.y >>> >>> On Mon, 2 Jun 2014, Shantanu Ghosh wrote: >>> >>>> Dear Anastasia and Freesurfer experts, >>>> I am trying to set up an analysis of motion parameters using the flag >> -q >>>> from a set of DTI Dicoms located on the Martinos cluster, but I am >>>> facing >>>> problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set >> to >>>> Freesurfer5.3 and FSL. >>>> What am I doing wrong? >>>> My config file is attached and here are my commands. >>>> cd /autofs/space/glia_001/users/shantanu/dtistudy/ >>>> setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH} >>>> setenv FSENV_KEEP_PROMPT >>>> setenv MNE_ROOT /usr/pubsw/packages/mne/stable >>>> setenv SUBJECTS_DIR >>>> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons >>>> setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0 >>>> source /usr/local/freesurfer/nmr-stable53-env >>>> source /usr/pubsw/packages/mne/stable/bin/mne_setup >>>> ----My console output----- >>>> glia:shantanu[120] mynmr53 >>>> -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> -------- >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>> WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does >> not >>>> exist >>>> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 >>>> FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast >>>> FSF_OUTPUT_FORMAT nii.gz >>>> SUBJECTS_DIR >> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons >>>> MNI_DIR /usr/local/freesurfer/stable5_1_0/mni >>>> FSL_DIR /usr/pubsw/packages/fsl/5.0.0 >>>> MNE software location set to: /usr/pubsw/packages/mne/stable MATLAB >> software not available >>>> /usr/pubsw/packages/mne/stable/bin already in PATH >>>> /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH >>>> /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to >>>> XUSERFILESEARCHPATH >>>> Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables >> correctly. >>>> Note: FreeSurfer environment is needed to access tkmedit from >>>> mne_analyze. >>>> glia:shantanu[121] trac-all -qa -s 008801 -c >>>> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt >>>> ERROR: >> flag -qa unrecognized >>>> -qa -s 008801 -c >>>> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt >> glia:shantanu[122] >>>> Thanks in advance for all help. >>>> Shantanu >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
