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
<ayend...@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
<ayend...@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
<ayend...@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
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.
--
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
