Hi Bruce and Alex.
We currently think we get more MR information by collecting T1/T2
multimodal scans for the
sake of tissue-type segmentation. We have a lot of data with T1/T2 and
0.5 mm voxels,
and even more data with T1/T2/PD and 1.015625 mm voxels. And we know how to
massively run these studies through a T1-only FreeSurfer run.
We would be >very< interested in helping with any >multi-modal<
atlas definition,
both the 'aseg' and 'aparc' cases. Any guidance you could provide for
running the
multi-modal tissue-classifier included in Freesurfer would be a big help.
Alex, you can't simply average T1 and PD since in T1, white matter looks
lighter than
gray matter, which looks lighter than csf, while with PD/T2, white
matter looks darkest,
and csf is bright white. Combining different kinds of spectral scales
permits the
tissue classification to be more specific and sensitive.
Greg Harris
University of Iowa Psychiatry Brain Imaging Lab
Hans Johnson wrote:
Please contact the freesurfer team (Bruce Fischl may be a starting point)
and see if we can help generate a multi-modal atlas tuned the T1/PD data
that we collect with our definitions of structures. This is really the only
way we can make fair comparisons between the methods.
Hans
Fornito, Alexander wrote:
Hi Bruce,
I've managed to dig up some images where we have both a T1 and PD for the same
person. Is the multi-channel segmentation implemeted in one of the dev
versions? Is it simply a mater of averaging the T1 and PD instead of multiple
T1s?
Thanks,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
________________________________
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 24/10/2005 10:19 PM
To: Fornito, Alexander
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] PDs?
Hi Alex,
unfortunately the current answer depends on what part of the brain you are
interested in. For cortex, it appears that the raw CNR of mp-rage is
significantly better than the multi-channel (T1/PD/T2*) CNR. On the other
hand, subcortically for things like pallidum/putament, the multi-channel
segmentation has much higher CNR.
We do have multi-channel aseg segmentation in place, but haven't used it a
ton (since we have so much mp-rage data around).
cheers,
Bruce
On Mon, 24 Oct 2005, Fornito, Alexander wrote:
Hi, We're about to start a longitudinal study and are keen to get
accurate measures of structural change. Currently we are planning to
acquire a T1 and T2, and have some spare time for another acuqisition.
I've noticed in a recent paper (Fischl, et al (2004) Neuroimage,23,
S69-S84) you discuss the benefits of combining T1 and PD images to aid
segmentation. Just wandering if there are any plans to incorporate
multichannel segmentation into freesurfer, and if so, would you recommed
acquiring two T1s and averaging, or a single T1 and PD? Thanks, Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
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