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 <martijnsteenw...@gmail.com<mailto:martijnsteenw...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Granberg, Erik Tobias Verzonden: vrijdag 15 januari 2016 21:15 Aan: freesurfer@nmr.mgh.harvard.edu<mailto: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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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