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 > > > -- 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.