Hi Greg and Bruce, I figure averaging the T1s and PDs would eliminate the contrast, just (incorrectly) figured that might be how the info would be combined in freesurfer if the multi-spectral segmentation was already included in the current dev versions.
From experience (and in line with Bruce's comments), 2 or more T1s seems to give more than enough contrast for the cortex. I was primarily interested in using the PDs for the subcortical aseg, as some of my labels seem too big. However, having followed your discussion on another thread, it seems that this may be due to the atlas labelling (eg., thalamus touching caudate) rather than an error in the algorithm for my images. Given that, I'm not sure the PD would add that much more ...
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Greg Harris [mailto:Gregory-Harris@uiowa.edu] Sent: Sat 29/10/2005 9:32 AM To: Fornito, Alexander; Bruce Fischl Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PDs?
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 alexander.fornito@wh.org.au
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] 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 alexander.fornito@wh.org.au
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