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
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