I'll let Doug chime in on that tool.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofield@yahoo.com] Sent: Saturday, August 12, 2017 6:54 AM To: Freesurfer support list Subject: Re: [Freesurfer] Mean diffusivity on cortex?
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting
the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.commailto:shane.schofield@yahoo.com> wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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