Is the lh.orig surface changing?
On 12/17/2020 5:53 PM, Ben Deen wrote:
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Hi all,
I'm encountering an issue with surface reconstruction quality in ventromedial
prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted
input data to recon-all. I'm using the following command, with Freesurfer 7.1.1
running on Mac OS 10.15.7 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551; the
options file specifies "mris_inflate -n 30"):
recon-all -s ${subject} -i T1w.nii.gz -all -hires -expert ${optsFile} -T2
T2w.nii.gz -T2pial
Across four participants I've tested with this approach, there is a consistent
reconstruction issue with the gyrus rectus and medial orbital gyrus, in which
they are cut off in the white and pial surfaces (see images at MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://www.dropbox.com/sh/crpcjro63bc6477/AADNtt9xJL1SV2kiaVJsGnSYa?dl=0<https://secure-web.cisco.com/1VsBngXjwYNdyCXm9WeFfxfF4NEiuvK0cksK70AaZdOGj9BgjNNYyCRhqEWxzPwHbUTEFALSIbTMlOUoi6CYeraUeGNIh0ZTIa-kr4hxUtjNp8nKL7M3zwQ2sccXeoVNOYNiGDHTLcfWWpWqQF1mgbsSEXDsctsyOoJs4RlDuDTu7RSxseti13BAo_AWXKp9NQ9bzh5Gma0QUI0B1GBHukq9qI055NRxtvw1B4n7sq2EcDgWGgVOf_YPj0KGYxcBroVofRBuyMR8C3bDrH8RvZg/https%3A%2F%2Fwww.dropbox.com%2Fsh%2Fcrpcjro63bc6477%2FAADNtt9xJL1SV2kiaVJsGnSYa%3Fdl%3D0>;
it's particularly clear against the T2 image). I've tried to correct the issue
by manually modifying wm.mgz to include all wm voxels in these gyri. However,
when I do so and rerun autorecon2-wm, the orig surface improves to incorporate
the edits to wm.mgz, but the white/pial surfaces do not. By debugging
individual steps of recon-all, I've found that the -white step seems to be to
blame for this: when I rerun this step, the output white.preaparc surface
doesn't change to incorporate my edits to wm.mgz.
Any thoughts as to what might be causing these issues - both the initial
reconstruction problem, and the failure to update with manual edits? There is
some signal dropout in the T1 image in this region, which may contribute to the
issue, although I would hope the T2 image could compensate for this.
Thanks,
Ben
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