I agree. Thank you so much, Matt, for helping me out with my analyses. If I ever see you at a conference, I'm totally buying you a drink :)
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Martin Kavec
Sent: Mon 3/30/2009 3:46 AM
To: [log in to unmask]
Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
Thanks a lot Matt for sharing your approach and experiences,
Best,
Martin
On Sunday 29 March 2009 00:48:22 Matt Glasser wrote:
> Well, I draw the ROI on the cortical surface in Caret and then map it to
> the volume, which makes a 1 voxel thick ROI in the voxels of the white
> matter surface. There are a number of ways to generate the white matter
> surface, however. Before I started using freesurfer, I used the FAST
> segmentations. I took the white matter mask from FAST, blurred it with a
> 3x3x3 voxel kernel, and then selected voxels with values between .50 and
> .85. This produced a white matter surface ribbon that is about 1 voxel
> thick. You could then find the intersection between your ROI and the
> ribbon to get the cortical ROI that is only in the first white matter
> voxel.
>
>
>
> I always correct for distortions (there are a variety of ways to do this, a
> phase up/phase down correction is best, but you can also use a field map or
> even use FNIRT to register your FA to your T1 and then apply the warpfield
> to your raw data). The issues I describe below occurred from tractography
> from ROIs in diffusion space. It is worse in some brains, or acquisitions
> than others, but I just choose to avoid it across all subjects, rather than
> make exclusion/termination masks on a case by case basis. I am not
> convinced that you get more information by tracking into the cortical grey
> matter, given the resolution of DTI, than you get from tracking up to the
> superficial white matter, and you can avoid errors this way.
>
>
>
> Peace,
>
>
>
> Matt.
>
>
>
> _____
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Martin Kavec
> Sent: Saturday, March 28, 2009 7:36 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>
>
>
> Hi Matt,
>
> On Fri, Mar 27, 2009 at 10:54 PM, Matt Glasser <[log in to unmask]> wrote:
>
> I always track from white matter. If it is a cortical ROI I use the 1st
> voxel of the white matter surface.
>
>
> That's an interesting approach. How do you get from cortical ROI to the 1st
> voxel of the WM?
>
>
> Honestly, I have found that tracking
> from/into cortical grey matter results in more error than useful
> information (its easy to get pathways crossing sulci for example, if you
> combine partial voluming with the fact that the principle diffusion
> direction in cortical grey matter is oriented perpendicular to the cortical
> surface, and cortical grey matter ROIs may be very close to brain rim
> voxels).
>
>
> Could this simply be because of the nonlinear distortions between DTI and
> FreeSurfer input image? It could be several voxels in most of the brain.
>
> Thanks,
>
> Martin
|