Hi again,
Thank you again for the response. We have been discussing such an approach as a backup plan if it is not possible to adjust the pial surface with manual interventions. It does not feel straightforward though as the lesion filling techniques have only been used in WM before (AFAIK). As you say, the intensities across the cortex can vary quite a lot as well so choosing the intensity to fill with is also problematic (although some sort of averaging of neighboring voxels to each lesion seems logical).
Kind regards, Tobias
_________________________________________ Tobias Granberg, MD, PhD
Post-doctoral research fellow Multiple Sclerosis Imaging Group MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging 149 13th St Charlestown, MA 02129
Resident in Radiology Karolinska University Hospital Stockholm, Sweden
On 15 jan 2016, at 16:10, Martijn Steenwijk <martijnsteenwijk@gmail.commailto:martijnsteenwijk@gmail.com> wrote:
In that case it may be better to apply some form of GM lesion filling. Studies have shown that (at least in FAST and SPM) WM lesions affect the GM segmentation throughout the brain (i.e. Chard et al, Gelinau-Morel et al, Battaglini et al) – and I have the feeling that the same is true for FreeSurfer. The reason is that the WM (and so the GM) distribution is slightly different as a result of the lesions, thereby the border of the GM is drawn slightly different compared to the normal situation. So I would try to fill the WM (and GM) lesions before running FreeSurfer. Note that estimating the proper local GM intensity may be challenging as there is a lot of intensity variation in the GM.
Best, Martijn
Van: Granberg, Erik Tobias [mailto:EGRANBERG@mgh.harvard.edu] Verzonden: vrijdag 15 januari 2016 21:59 Aan: martijnsteenwijk@gmail.commailto:martijnsteenwijk@gmail.com; Freesurfer support list Onderwerp: Re: [Freesurfer] Cortical MS lesions - correcting pial surfaces
Hi Martijn,
Thank you for the response! I believe you are right that it is a complex problem. It is true that the GM/WM border can sometimes by hard to identify in type I (leukocortical) lesions, but in in purely intracortical lesions, it is still readily identifiable. We also have corresponding 7T scans to help guide our edits. In this case we are specifically interested in looking at the relationship of cortical pathology and cortical thickness and are therefore still looking for a possible workaround.
Kind regards, Tobias
On 15 jan 2016, at 15:49, Martijn Steenwijk <martijnsteenwijk@gmail.commailto:martijnsteenwijk@gmail.com> wrote:
I do not think it is easy to solve the problem, because often it is unknown were the exact GM/WM border is in the lesion. Manual editing may introduce a bias to the CT, so probably it is better to leave it as a limitation of the method.
Best, Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Granberg, Erik Tobias Verzonden: vrijdag 15 januari 2016 21:15 Aan: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] Cortical MS lesions - correcting pial surfaces
Dear FreeSurfer colleagues,
We’re working with MS data and wanted your input on how we could best handle patients with extensive cortical pathology causing inaccurate reconstructions of the surfaces. In short the pial surfaces “dips” in too deep towards the WM surface due to the T1-hypointensity.
A lot of the problems can be mediated by doing wm.mgz edits and actually including the lesioned tissues, which pushes out both surfaces to an accurate position. Sometimes though, the cortical lesion affects the whole depth of the surface and this trick does not help.
Is there any way to directly push out or “anchor” the pial surface?
Thank you for the help!
Kind regards, Tobias
Post-doctoral research fellow Multiple Sclerosis Imaging Group MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging 149 13th St Charlestown, MA 02129 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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