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Hi Douglas,

Thank you for your reply,

The area to the left of the cursor is a wm hypointensity label and the one to the right (lighter pink) is the lingual gyrus,

If you look at other areas in the left hemisphere you can also see places where the sulci haven’t been picked up that don’t have wm hypointensity labels,

BW Andrea

On 3 Oct 2021, at 14:03, Douglas N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> wrote:

I can't tell what is going on there. Is the pink point by your cursor the lingual coming in or is it a hypointensity label?

On 9/28/2021 2:19 PM, McKavanagh, Andrea [amckav] wrote:

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Hi all,

I am having a problem with some post recon-all edits.

The white matter in some of my scans has been over estimated in the aparc+aseg file, labelling some of the white matter (e.g by the lingual gyrus) as hypointensities and/or missing out many sulcui entirely (figure 1).

However, the wm.mgz file is accurate picking up only the correct white matter in these areas (figure 2).

This is happening, on most of the scans I have processed with recon-all. I am using Freesurfer 7.2.0 on Mac BigSur and have ran the same scans through previous version of Freesurfer (6/7.1) with the same problem occurring.

I have read on the archives this has previously been a bug in another version, is this the case here? Or is there another correction step I could try? Any suggestions are welcome :)

Thanks, BW Andrea

<Screenshot 2021-09-28 at 17.19.17.png><Screenshot 2021-09-28 at 17.19.36.png>

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