NIH

On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it.

So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too.

Good luck!

a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia,   Thank you! I can see that the aparc+aseg spilled over badly. I am
going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original
image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep
you and the FS community updated on the results, in case anybody is curious.

Sincerely,
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
wrote:

Hi Susie - The -tv (tract volume) option of freeview is designed
specifically to display the merged*.mgz output files of tracula. For a
regular volume, use -v or no option at all. For best displaying the
aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
map menu.

Hope this helps,
a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia,   I'm attaching the graphic I arrived at with
the command:

> freeview -tv <subjectID>/dlabel/diff/aparc+aseg.flt.nii.gz
-v
<subjectID>/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the
subjectID. I could not detect
spill over in these images, mostly because the frontal lobe is
a little cut off. Did
you perhaps use a different viewer? I'm hoping to be able to
detect these
mis-registrations better for myself in the future. Thanks for
all your help!

Sincerely,
Susie Kuo
NIH

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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--
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Mediocrity knows nothing higher than
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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

--
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

Susie Kuo

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