Dear Anastasia,

I wrote to the Freesurfer Listserv yesterday about the problem I am facing in running tracula, although my FS is set to version 5.3.

However, I debugged some problems in the config file, and now trac-all -prep runs through all the DTI volumes, but exits with errors. Also, it does not recognize the -qa flag. What am I doing wrong?

Attached is the log file, and an updated config file.

Any help is highly appreciated.

Thanks. Shantanu

---------------------------- Original Message ---------------------------- Subject: TRACULA: ERROR in -qa Flag From: "Shantanu Ghosh" shantanu@nmr.mgh.harvard.edu Date: Mon, June 2, 2014 6:32 pm To: freesurfer@nmr.mgh.harvard.edu --------------------------------------------------------------------------

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