Re: [Freesurfer] Gray matter segmentation
Hi Maxime what does the aseg look like in that region? The pial surface gets "frozen" adjacent to the cc (so it is fixed to be in the same location as the white). Maybe the cc if off by a bit? cheers Bruce On Sat, 23 Feb 2019, Maxime Perron wrote: External Email - Use Caution Dear Freesurfer experts, I use Freesurfer 6 on macOS Sierra 10.12.6. I noticed a potential error in some of my participants. In fact, there seems to have an error in the segmentation of gray matter. You will find attached pictures of the segmentation. I am wondering if it is an error and if anyone has any idea to fix it. I think it affects the surfaces. Thank you, Maxime Perron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gray matter segmentation
Can you tar up and upload the subjects to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when they are there On 3/4/19 4:59 PM, Maxime Perron wrote: > > External Email - Use Caution > > Hi Freesurfer Experts, > > > I was wondering if you have had time to look at my problem? > > > Cheers, > > Maxime > > > *De :* Maxime Perron > *Envoyé :* 26 février 2019 14:26 > *À :* Freesurfer support list > *Objet :* Re: [Freesurfer] Gray matter segmentation > > Hi Bruce, > > Thanks a lot for your quick answer. In the aseg, the gray matter in > this region is not labelled. I've attached two cases of such error in > the participants. > > In the first participant (S156), the cc seems to be O.K., yet the gray > matter is not labelled. I tried to correct the aseg but the > segmentation doesn’t change: indeed, the modification does not seem to > have been taken into account after the recon-all -noaseg, even after > modifying both the aseg and the aseg.presurf. > > In the second participant (S115), the cc is mislabelled, and it’s > probably what causes the error of segmentation and gray matter labelling. > > All in all, I have two patterns of error. Do you have any > modifications in mind that could solve these issues? > > Thank you very much in all cases! > > Maxime > > > >> On Feb 24, 2019, at 8:14 PM, Bruce Fischl > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> Hi Maxime >> >> what does the aseg look like in that region? The pial surface gets >> "frozen" adjacent to the cc (so it is fixed to be in the same >> location as the white). Maybe the cc if off by a bit? >> >> cheers >> Bruce >> On Sat, 23 Feb 2019, Maxime Perron wrote: >> >>> External Email - Use Caution >>> Dear Freesurfer experts, >>> >>> I use Freesurfer 6 on macOS Sierra 10.12.6. I noticed a potential >>> error in some of my participants. In >>> fact, there seems to have an error in the segmentation of gray >>> matter. You will find attached pictures >>> of the segmentation. I am wondering if it is an error and if anyone >>> has any idea to fix it. I think it >>> affects the surfaces. >>> >>> Thank you, >>> Maxime Perron >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gray matter segmentation
External Email - Use Caution Hi Greve, I uploaded my data to the ftp site, Thanks, Maxime De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Greve, Douglas N.,Ph.D. Envoyé : 6 mars 2019 18:26 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Gray matter segmentation Can you tar up and upload the subjects to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when they are there On 3/4/19 4:59 PM, Maxime Perron wrote: > > External Email - Use Caution > > Hi Freesurfer Experts, > > > I was wondering if you have had time to look at my problem? > > > Cheers, > > Maxime > > > *De :* Maxime Perron > *Envoyé :* 26 février 2019 14:26 > *À :* Freesurfer support list > *Objet :* Re: [Freesurfer] Gray matter segmentation > > Hi Bruce, > > Thanks a lot for your quick answer. In the aseg, the gray matter in > this region is not labelled. I've attached two cases of such error in > the participants. > > In the first participant (S156), the cc seems to be O.K., yet the gray > matter is not labelled. I tried to correct the aseg but the > segmentation doesn’t change: indeed, the modification does not seem to > have been taken into account after the recon-all -noaseg, even after > modifying both the aseg and the aseg.presurf. > > In the second participant (S115), the cc is mislabelled, and it’s > probably what causes the error of segmentation and gray matter labelling. > > All in all, I have two patterns of error. Do you have any > modifications in mind that could solve these issues? > > Thank you very much in all cases! > > Maxime > > > >> On Feb 24, 2019, at 8:14 PM, Bruce Fischl > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> Hi Maxime >> >> what does the aseg look like in that region? The pial surface gets >> "frozen" adjacent to the cc (so it is fixed to be in the same >> location as the white). Maybe the cc if off by a bit? >> >> cheers >> Bruce >> On Sat, 23 Feb 2019, Maxime Perron wrote: >> >>> External Email - Use Caution >>> Dear Freesurfer experts, >>> >>> I use Freesurfer 6 on macOS Sierra 10.12.6. I noticed a potential >>> error in some of my participants. In >>> fact, there seems to have an error in the segmentation of gray >>> matter. You will find attached pictures >>> of the segmentation. I am wondering if it is an error and if anyone >>> has any idea to fix it. I think it >>> affects the surfaces. >>> >>> Thank you, >>> Maxime Perron >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
