Hi Mario, I'm not sure what an N4 correction is, but the Freesurfer team helped me to solve the problem. Here are their instructions:
Sometimes when the skullstrip is wrong, it affects the surfaces even if the wm parcellation is correct. I ran -skullstrip with the watershed parameter of 30, and then reran the subject with -autorecon2 -autorecon3. You can find info how how to run watershed here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix>I hope this helps! I can send over our full conversation if this doesn't give you the information you need. Allie On Fri, May 13, 2011 at 4:26 PM, Mario Ortega <mario.ort...@gmail.com>wrote: > HI Allie, > I am having this exact issue, and I was able to fix only a few of them, Did > the Freesurfer team ever give you a reliable fix? I used an N4 correction > before the entire FS process. > -Mario > > > On Wed, Apr 20, 2011 at 8:32 AM, Allie Rosen <rosen.al...@gmail.com>wrote: > >> Hi, >> >> Do you want me to email you in a few days about this? >> >> Allie >> >> >> >> >> On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen >> <k...@nmr.mgh.harvard.edu>wrote: >> >>> Got it. I'll look at it and get back to you. >>> >>> >>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>>> >>>> http://dl.dropbox.com/u/14127241/C42.tar.gz >>>> >>>> Here is the link to the subject. I hope this works!! >>>> >>>> Allie >>>> >>>> >>>> >>>> On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguyen <k...@nmr.mgh.harvard.edu >>>> >wrote: >>>> >>>> Another way you can try is upload it to your google doc account and >>>>> send me >>>>> the link. Someone did that before. >>>>> >>>>> >>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>> >>>>> Hi, >>>>> >>>>>> >>>>>> No, I'm not from the centre. I'm working on putting the files in >>>>>> Dropbox >>>>>> and >>>>>> sending you a link to them, because apparently I don't have ftp >>>>>> access. >>>>>> >>>>>> Allie >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen < >>>>>> k...@nmr.mgh.harvard.edu >>>>>> >>>>>>> wrote: >>>>>>> >>>>>> >>>>>> Are you from the center? If so you can just cd into /space/outgoing >>>>>> and >>>>>> >>>>>>> copy your file there. If not, you can follow the instructions in the >>>>>>> box >>>>>>> at >>>>>>> the top using a terminal. >>>>>>> >>>>>>> >>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> >>>>>>>> I'm really sorry, but I don't understand those instructions. Do I >>>>>>>> login >>>>>>>> to >>>>>>>> the freesurfer website? Or do I login through a terminal somehow? Do >>>>>>>> I >>>>>>>> type >>>>>>>> the stuff in the boxes into the terminal? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Allie >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen < >>>>>>>> k...@nmr.mgh.harvard.edu >>>>>>>> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>> Hi Allie, >>>>>>>> >>>>>>>> >>>>>>>>> You can compress the subject dir and upload it following the >>>>>>>>> instructions >>>>>>>>> here >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>> >>>>>>>>> Hi Khoa, >>>>>>>>> >>>>>>>>> >>>>>>>>> How do I upload subjects? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Allie >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen < >>>>>>>>>> k...@nmr.mgh.harvard.edu >>>>>>>>>> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Allie, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Can you upload the subject? I'll take a look and see if I can >>>>>>>>>>> figure >>>>>>>>>>> out >>>>>>>>>>> what's wrong. >>>>>>>>>>> >>>>>>>>>>> -Khoa >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> This (recon-all after wm.mgz and brainmask.mgz edits) didn't >>>>>>>>>>> work. >>>>>>>>>>> >>>>>>>>>>>> The >>>>>>>>>>>> part >>>>>>>>>>>> that wasn't included in the pial or white matter surfaces is >>>>>>>>>>>> still >>>>>>>>>>>> not >>>>>>>>>>>> included. The intensities in the white matter regions are no >>>>>>>>>>>> different >>>>>>>>>>>> than >>>>>>>>>>>> in white matter regions that were included in the white matter. >>>>>>>>>>>> Any >>>>>>>>>>>> other >>>>>>>>>>>> suggestions? >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Allie >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen < >>>>>>>>>>>> rosen.al...@gmail.com >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I am running recon-all tonight using wm voxels that I manually >>>>>>>>>>>> >>>>>>>>>>>>> added >>>>>>>>>>>>> (I >>>>>>>>>>>>> also edited brainmask.mgz to add missing grey matter). To me it >>>>>>>>>>>>> doesn't >>>>>>>>>>>>> really look like a case of the white matter not having a high >>>>>>>>>>>>> enough >>>>>>>>>>>>> intensity. It simply looks like the whole lobe was ignored, >>>>>>>>>>>>> regardless >>>>>>>>>>>>> of >>>>>>>>>>>>> intensity. But I'll check tomorrow to see if the intensity is >>>>>>>>>>>>> low. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Allie >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl < >>>>>>>>>>>>> fis...@nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> What is the intensity of the white matter in the regions you >>>>>>>>>>>>> drew >>>>>>>>>>>>> in? >>>>>>>>>>>>> A >>>>>>>>>>>>> >>>>>>>>>>>>> couple of control points might help if it is less than 110 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Apr 18, 2011, at 12:36 PM, Allie Rosen < >>>>>>>>>>>>>> rosen.al...@gmail.com> >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for all the responses! I've actually had the same >>>>>>>>>>>>>> problem >>>>>>>>>>>>>> for >>>>>>>>>>>>>> multiple subjects. I'm using version 5.0.0. I'll try fixing >>>>>>>>>>>>>> the >>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>> as well. I've attached pictures of where I am adding wm >>>>>>>>>>>>>> voxels. >>>>>>>>>>>>>> They >>>>>>>>>>>>>> aren't >>>>>>>>>>>>>> really in the same places as in the online tutorials. Could >>>>>>>>>>>>>> you >>>>>>>>>>>>>> take >>>>>>>>>>>>>> a >>>>>>>>>>>>>> quick >>>>>>>>>>>>>> look to see if they're in the right place? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Allie >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori << >>>>>>>>>>>>>> s...@nmr.mgh.harvard.edu> >>>>>>>>>>>>>> s...@nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> pial surface which looks like this can only be corrected by >>>>>>>>>>>>>>> correcting >>>>>>>>>>>>>>> the wm.mgz. Also I would suggest to try and fix the >>>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> see >>>>>>>>>>>>>>> if it >>>>>>>>>>>>>>> corrects the surfaces as well. Since part of the cerebellum >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> stripped >>>>>>>>>>>>>>> off, >>>>>>>>>>>>>>> it's probably affecting the segmentation as well but I could >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> wrong. >>>>>>>>>>>>>>> what >>>>>>>>>>>>>>> version of freesurfer are you using. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Can I still add voxels to wm.mgz even though the points >>>>>>>>>>>>>>> would be >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> outside >>>>>>>>>>>>>>>> even the pial boundary? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> Allie >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>>>>>>>>>>>>>>> < <s...@nmr.mgh.harvard.edu>s...@nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> This probably needs white matter edits but it's hard to >>>>>>>>>>>>>>>> tell >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>> slice. Please refer to our white matter edits wiki and >>>>>>>>>>>>>>>>> toplogical >>>>>>>>>>>>>>>>> defects >>>>>>>>>>>>>>>>> wiki and see if it helps in fixing the errors in your >>>>>>>>>>>>>>>>> datasets. >>>>>>>>>>>>>>>>> Also >>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>> looks like part of the Cerebellum is stripped off. You >>>>>>>>>>>>>>>>> might >>>>>>>>>>>>>>>>> want >>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> correct >>>>>>>>>>>>>>>>> that as well. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Once processed, several of my subjects have had errors >>>>>>>>>>>>>>>>> around >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> occipital >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lobe. Attached is an example. I've already tried editing >>>>>>>>>>>>>>>>>> brainmask.mgz >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> running recon-all, but as you can see, this didn't change >>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>> pial >>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>> wm >>>>>>>>>>>>>>>>>> borders. What can I do to fix this? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Allie Rosen, MSc Candidate >>>>>>>>>>>>>>>>>> Graduate Student, Department of Neurosurgery >>>>>>>>>>>>>>>>>> Toronto Western Hospital 14-327 >>>>>>>>>>>>>>>>>> 399 Bathurst St. >>>>>>>>>>>>>>>>>> University of Toronto >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 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> >>>>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> <2.png> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> <3.png> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> 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 >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. 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