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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>
>
>


-- 
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



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