sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Sounds great, thanks again for your help and will try out your > recommendations. > Have a great day! > > 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 4:27 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > 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 > _______________________________________________ > 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
