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" <shant...@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
--
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
--
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
ErrorLogFile_007501
Description: Binary data
setenv SUBJECTS_DIR /autofs/cluster/transcend/MRI/WMA/recons
set dtroot = /autofs/space/glia_001/users/shantanu/dtistudy
set subjlist = ( 007501)
set dcmroot = /autofs/cluster/transcend/MRI/WMA/DICOM
set dcmlist = ( 005801/108000-000014-000001.dcm \
007501/823000-000012-000001.dcm )
set bvecfile = /autofs/cluster/transcend/MRI/WMA/dti/008801/bvecs
set bvalfile = /autofs/cluster/transcend/MRI/WMA/dti/008801/bvals
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
set cvstemp = cvs_avg35
set cvstempdir = $FREESURFER_HOME/subjects
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
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