Alright I converted the COR files to mgz fine, and saved the volume as brainmask.mgz. All looks good. But before I run -autorecon2, am I going to run into problems because I only have a brainmask.mgz and not a brainmask.auto.mgz? (I deleted the old brainmask.auto.mgz because it was the old volumes before I corrected them manually). I just want to make sure I am good to run -autorecon2 before I go ahead and begin it.
Quoting Bruce Fischl <[EMAIL PROTECTED]>: > but you'll need to convert the COR file you saved to brainmask.mgz if > you > want to recover your edits (4 hours of manual editing!). > > Bruce > > On Wed, 28 Jun > 2006, Nick Schmansky wrote: > > > The brainmask.mgz file is the one that should be edited (and > saved), so > > select that filename to save. Then just continue with autorecon2 > (and > > it will use your brainmask.mgz). It will not overwrite your > > brainmask.mgz unless you specify the aptly named '-clean-bm' flag > to > > recon-all. > > > > > > On Wed, 2006-06-28 at 15:00 -0400, [EMAIL PROTECTED] wrote: > >> I just finished my 4 hour manual editing...went to file>save > volume > >> as...then saved it to where it defaulted me, which was the mri > folder of > >> this subject. When i pull up my brainmask, it is giving me the > same one > >> that it had before i made any changes. I hope i didnt do > something > >> wrong and lost all the edits. There is 256 COR files though now > in my > >> mri folder for this subject I noticed. Maybe these are the > edited > >> slices? Just let me know how to get my final brainmask and how > to > >> proceed with running -autorecon2 on it properly. Thanks. > >> > >> Quoting Bruce Fischl <[EMAIL PROTECTED]>: > >> > >>> it helps detect cases in which the deformation is too big (e.g. > when > >>> the > >>> surface deforms all the way into the cerebellum), and can thus > >>> recover from > >>> e.g. cerebellum chopping. > >>> > >>> On > >>> Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote: > >>> > >>>> I am currently in the process of manual editing...just curious > >>> though, > >>>> what exatly does adding an atlas do to the skullstrip process? > >>>> > >>>> Quoting Nick Schmansky <[EMAIL PROTECTED]>: > >>>> > >>>>> First have a look at the troubleshooting wiki pages at: > >>>>> > >>>>> > >>> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData > >>>>> > >>>>> In particular, Subject 1 has a skull strip problem, and the > fix > >>> info > >>>>> is > >>>>> here: > >>>>> > >>>>> > >>> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix > >>>>> > >>>>> I'm guessing you have seen this page since you have already > >>>>> attempted > >>>>> one type of fix (adjusting the watershed parameters). The > >>>>> alternative > >>>>> fix is the slice-by-slice manual editing. > >>>>> > >>>>> You could also try adding the wsatlas flag: > >>>>> > >>>>> recon-all -s (subject) -skullstrip -wsatlas > >>>>> > >>>>> which will use an atlas to help with the skull-strip. > >>>>> > >>>>> Does the contrast of your image look good? That is, comparing > >>> your > >>>>> orig.mgz to that of the sample subject 'bert' included with > >>>>> freesurfer? > >>>>> > >>>>> Nick > >>>>> > >>>>> > >>>>> On Wed, 2006-06-28 at 10:09 -0400, [EMAIL PROTECTED] wrote: > >>>>>> I am having trouble with one of my skull strips, and getting > >>> very > >>>>>> extreme results. When I re-run the skullstrip using > different > >>>>> watershed > >>>>>> values, anything at 56% or below takes 75%+ of the brain out, > >>> and > >>>>> as > >>>>>> soon as I jump to 57% or higher, it leaves on almost all of > the > >>>>> skull, > >>>>>> except for maybe 5% of it. Is this indicative of a more > >>>>> complicated > >>>>>> problem, and what is my next step (other than manually taking > >>> off > >>>>> the > >>>>>> skull), if any? > >>>>>> Thanks > >>>>>> _______________________________________________ > >>>>>> 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 > >> > >> > > > > _______________________________________________ > > 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
