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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 https://secure-web.cisco.com/1YjHwYMb6FHlCVkbgjtpceoj_IZMMa8YVArerusSJpfEDYC... 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
Is the lh.orig surface changing?
On 12/17/2020 5:53 PM, Ben Deen wrote:
External Email - Use Caution
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=0https://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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Yes, the lh.orig is changing, but not lh.white. (I responded to this on the 23rd, but the reply didn't show up in the archive and I'm not sure it went through, so I'm trying again.) Thanks,
Ben
On Wed, Dec 23, 2020 at 12:37 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Is the lh.orig surface changing?
On 12/17/2020 5:53 PM, Ben Deen wrote:
External Email - Use CautionHi 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://secure-web.cisco.com/1KDV2kh1hFklnQEMo3A3OhIninCwshEtcoVi9TnJNC0fL00... 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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Ben Deen -
Greve, Douglas N.,Ph.D.