Hi Ruth - If you download the update and unzip it, you'll see an executable called dmri_motion. You can run it without any arguments to see the help text.

Try something like this: dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out output.txt

a.y

On Fri, 13 Dec 2013, Ruth Carper wrote:

Thanks.  We haven't yet implemented TRACULA but have run eddy_correct on all the brains in our existing pipeline and still have the ecc.log files.  Is there a command line that would let us generate your motion measures without running TRACULA?

--Ruth

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From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Ruth Carper rcarper_99@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 8:28 PM Subject: Re: [Freesurfer] New features in TRACULA

Hi Ruth - Glad to hear this is useful to you. The rotation and translation parameters are extracted from the affine registration of each DWI volume to the first volume, which in trac-all is performed by eddy_correct.

a.y

On Tue, 10 Dec 2013, Ruth Carper wrote:

...

Hi Anastasia, We discussed your paper at our lab meeting yesterday so this was perfect timing on the release of motion measures in  your updated TRACULA.  But I wasn't clear where the numbers are coming from in your new update.  Is

this

...

from EDDY? eddy_correct?  Some other registration step?   Thanks, Ruth

...

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