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 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.
