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/SkullStripFixI 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.ortega@gmail.comwrote:
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.allie@gmail.comwrote:
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 khoa@nmr.mgh.harvard.eduwrote:
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 <khoa@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 < khoa@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 < >> khoa@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 < >>>> khoa@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.allie@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 < >>>>>>> fischl@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.allie@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 << >>>>>>>> sita@nmr.mgh.harvard.edu> >>>>>>>> sita@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 >>>>>>>>>> < sita@nmr.mgh.harvard.edusita@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. 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@nmr.mgh.harvard.edu
-
Allie Rosen