Hi Ruth - It's possible that your scans don't have any slices with excessive intensity drop-out. You can gauge that visually, by checking if there are any slices that are much darker than their neighbors.
Any operation that performs interpolation on the image intensity values, and thus smooths the images, will affect estimates of intensity drop-out. To what extent exactly, it's impossible to guess. You can just try running them before the bias field correction and see what happens.
a.y
PS: Please send all tracula-related emails to the freesurfer list and not to me only. The freesurfer list gets archived so that users can search for answers and we can avoid replication of questions. Thanks!
On Wed, 18 Dec 2013, Ruth Carper wrote:
So the images should be prior to bias field correction as well? I ran it on images post bias field correction (but pre eddy_correct) and your dropout measures (3rd and 4th values) were 0 and 1 respectively for every brain. --Ruth
From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Ruth Carper rcarper_99@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 18, 2013 8:06 AM Subject: Re: [Freesurfer] New features in TRACULA
Hi Ruth - If you apply the same mask to all the volumes in the DWI series, it's not a problem. The important thing is not to have applied any operation that would change the intensities of the images inside the brain. So these should NOT be the DWIs after the eddy_correct step, they should be before it.
a.y
On Tue, 17 Dec 2013, Ruth Carper wrote:
Thanks! I was able to run that with no problem. But as I read the wiki closely I notice that with your TRACULA pipeline dmri_motion is processing images that are still skull-on. Any thoughts on whether your algorithms would work properly if the skull was removed prior to eddy correction? I would think the rotation and translation measures would still be fine, but
I
don't know how you've automated the 2 measures of signal dropout. My dwi file is also skull removed. --Ruth
_
From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Ruth Carper rcarper_99@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 17, 2013 1:28 PM Subject: Re: [Freesurfer] New features in TRACULA
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
_
_
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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Anastasia Yendiki