yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> > Hi Bruce, > Thanks so much for the feedback, that is very helpful. We'll try deleting the > control points then. Is there a quick way to rerun recon-all without having > it take up to 5-8 hours? > > Also, a separate question, when running autorecon, after edits to the white > matter and pial surfaces, should we run the command -autorecon2 -autorecon3, > or would that include too many steps? I read that it's recommended to run > from -autorecon2-cp instead? > > > Thanks so much for your help, > B > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, December 01, 2016 4:04 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > the problme is that you have several control points in voxels that aren't > entirely wm. For example, 129, 134, 173 is a control point and it has no wm > in it. This causes the intensity in that region to go up way too high, as > we will normalize the control points to the desired wm intensity (110). I > ran it without any control points and it worked pretty well. You should > probably get rid of your control.dat. If you think that those thin frontal > strands should go out a bit further, since some voxels that are entirely > white matter (e.g. 134, 135, 162) but have an intensity that is less than > 110 (this one is 103 after normalizating) and it will bring the intensity > up a bit in that entire region (by the ratio of 110/103). > > On Thu, 1 Dec 2016, Rizvi, Batool wrote: > >> Hi Bruce, >> Thanks for your reply. It is actually brighter on the brainmask.mgz than the >> orig.mgz when I checked. I'm uploading the freesurfer subject here. >> >> Thanks! >> BR >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 01, 2016 2:31 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] white matter segmentation incorrect after >> intensity change >> >> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not >> really possible to diagnose from a single slice from a single subject. If >> you tar, gzip and upload the subject one of us will take a look >> >> cheers >> Bruce >> On Thu, 1 >> Dec 2016, Rizvi, Batool wrote: >> >>> >>> Hi FreeSurfer experts, >>> >>> >>> >>> After running -autorecon2 and -autorecon3, we're seeing issues for some of >>> the subjects, which now start showing changes in intensity/brightness in >>> some voxels, and this increased intensity is now missed by the white matter >>> and grey matter segmentation, and is labeled as non-brain matter. >>> >>> >>> >>> Attached is an example of a subject's brain that was segmented incorrectly, >>> which we think is due to the intensity around that frontal region. We hadn't >>> added control points in that region, so we are unsure what the cause of the >>> intensity change is. In our first pass before running -autorecon2 >>> -autorecon3, we did not notice this error or the intensity values to be so >>> bright for that region. >>> >>> >>> >>> Thanks for your help! >>> >>> BR >>> >>> >>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > 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
