Hi Martin,
I will have to defer to Bruce or Doug regarding the validity of analyzing FreeSurfer output for your subject - although I would not recommend any analysis on the current state of your subject's surfaces. After glancing at your data, I have a few recommendations: 1. You seem to be using an excessive number of control points. Control points are designed for diffuse intensity normalize - using too many control points is unnecessary and possibly counterproductive. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0?highlight=%28control%29%7C%28point%29 for more information on control points. 2. I've noticed that your brainmask.mgz is missing a large portion of your subject's cerebellum. This most likely caused some issues down the recon-all pipeline so you should address this issue first. You can change the watershed value to adjust the brain extraction. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 for information of fixing a bad skull strip. 3. Since the wm.mgz has done such a poor job of identifying white matter, I would suggest directly editing the wm.mgz. Of course, only edit the wm.mgz after first attempting to use (fewer) control points on a better skull-stripped brainmask.mgz. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for information on editing the wm.mgz. Best, Bram ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin <martin.loeff...@zi-mannheim.de> Sent: Saturday, December 23, 2017 4:26:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Dear Bruce, Dear Bram, Thanks a lot for having a look. Unfortunately the left hemisphere is equally important as the right one for our question of interest. With a lot of patience the recon-all has finished and the result looks surprisingly ok. I have additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after setting control points to correct errors in the wm.mgz. Some errors were corrected, but not all. Next I would like to correct the surfaces. My questions: - I know that recon-all is not designed for such a subject. But is there any argument against continuing the analysis now? - What can I do for those errors where the wm.mgz is still false, despite control points? I have uploaded the respective files. Best, Martin Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram Ryder Gesendet: Mittwoch, 13. Dezember 2017 23:23 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin, We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the right hemisphere. Best, Bram ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Loeffler, Martin <martin.loeff...@zi-mannheim.de<mailto:martin.loeff...@zi-mannheim.de>> Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Dear Bruce, I have uploaded the respective files. If there is something missing let me know. Cheers, Martin -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Dezember 2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help cheers Bruce On Tue, 12 Dec 2017, Loeffler, Martin wrote: > Dear Bruce, > > thanks for the quick reply! You are right, of course. I do find errors in > lh.inflated.nofix. > I have attached a screenshot of the biggest errors I found.. > Can you maybe guide me a little how to fix the issue? Do I just cancel the > running recon-all process, and set control points and run again? Investing > some time in manual editing would be fine as it's a case study... > > Thanks for your help, > Martin > > > ________________________________________ > Von: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von > "Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: Montag, 11. Dezember 2017 22:47 > An: Freesurfer support list > Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst > > Hi Martin > > a defect that large means that something big went wrong (skull or dura > attached, etc...). Try looking at the ?h.orig.nofix and/or the > ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find > defect 9 > > cheers > Bruce > > > On Mon, 11 Dec 2017, Loeffler, Martin wrote: > >> >> Dear FreeSurfer team, >> >> >> >> For a case report I'm running recon-all on a patient with a giant >> arachnoid cyst in the left hemisphere. It gets stuck at this point (last >> message): >> >> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) >> >> XL defect detected... >> >> It is stuck here since a whole day now, so I'm not expecting it to >> advance. >> >> Following this post: >> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I >> looked at the wm.mgz, but did not find huge errors. >> >> Do you have any ideas what the problem might be or what I can do to work >> around it? >> >> >> >> Thanks, >> >> Martin >> >> >> >> >> >> >> _______________________________________________ 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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