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