or in your case dave, just: cp brainmask.mgz brainmask.auto.mgz
since you manually edited brainmask.mgz On Thu, 2006-06-29 at 14:18 -0400, Doug Greve wrote: > > I'm not sure what will happen. Safest to just recreate it: > > cd subject/mri > mri_watershed T1.mgz brainmask.auto.mgz > > > [EMAIL PROTECTED] wrote: > > 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 > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
