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 <ayend...@nmr.mgh.harvard.edu>
To: Ruth Carper <rcarper...@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 <ayend...@nmr.mgh.harvard.edu>
> To: Ruth Carper <rcarper...@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 <ayend...@nmr.mgh.harvard.edu>
> > To: Ruth Carper <rcarper...@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
> >
> > >
> > >
> > >
> >
> >
> > The information in this e-mail is intended only for the person to whom
it
> is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
> >
>
>
>
>
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