On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.

a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia,
I see what you mean. I had previously used the dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
freeview. I didn't end up with the same images as you, however. Can you tell
me which images you used to obtain this overlay?

I am going to run bbregister tonight, and I'll let you know how it goes --
I'm hopeful!

Thank you again!

Susie Kuo
NIH

On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Susie - I'm attaching a snapshot from your subject, showing
the aparc+aseg overlaid on the FA map. The registration has
failed. The frontal lobe has spilled out of the brain, the white
matter has spilled into the ventricles.

I strongly recommend using bbregister for the intra-subject
registration, which is the default in the latest version of
trac-all.

Hope this helps,
a.y

On Tue, 26 Mar 2013, Susan Kuo wrote:

Hi Anastasia, I did as you recommended and checked
the diffusion-to-anatomical
registration, and the overlay of aparc+aseg_mask on
FA, and these views seem to be
good. Upon closer inspection, what I find is that
there are incipient 'bits' of all
the tracts, but they seem to not have 'grown',
though they are in the proper space
(comparing them to good brains that yielded the full
complement of tracts). Is there a
configuration in your TRACULA that controls the
growing of the tracts specifically?
Perhaps I should look into that.

Thank you, btw, for your very prompt reply
yesterday- it was much appreciated!

Sincerely,
Susie Kuo
NIH

On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>
wrote:

Hi Susan - Good to hear that you get good
results for most of your
subjects. Have you checked the aparc+aseg and
the diffusion-to-anatomical
registration for the subjects that are
failing? I'd check the
aparc+aseg_mask (in the dlabel/diff directory)
over the FA map to see if
there are any holes or misregistration.

a.y

On Mon, 25 Mar 2013, Susan Kuo wrote:

Hi FreeSurfers and Anastasia, TRACULA
is working great for
me, generating tracts for a sample of 20
subject
brains I'm working with. However, for 3
of the brains, I'm
receiving incomplete and poorly formed
tracts.
I've re-run trac-all at least 2x on each
subject in case there
was a mistake in my original
configuration.
However, I am reproducing the same
results. Does anybody have
an idea why I would see these "spotty"
tracts?

Thank you for all your help!

--
Susie Kuo
NIH

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--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear

Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear