Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
It is a defect of some kind. Use the save point / goto feature of tksurfer and tkmedit, as described in the tutorial, to see discover the cause of the defect. That is, click on a point on that needle in tksurfer, click save point, then click goto point in tkmedit, after loading the brainmask and whitematter surfaces. Probably some dura is remaining.
Nick
On Fri, 2008-08-15 at 10:52 +0800, 李日 wrote:
Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually, it wouldn't be dura because of the location. Load the parcellation data, and if its in the 'Unknown' region, it can be ignored.
Nick
On Thu, 2008-08-14 at 23:00 -0400, Nick Schmansky wrote:
It is a defect of some kind. Use the save point / goto feature of tksurfer and tkmedit, as described in the tutorial, to see discover the cause of the defect. That is, click on a point on that needle in tksurfer, click save point, then click goto point in tkmedit, after loading the brainmask and whitematter surfaces. Probably some dura is remaining.
Nick
On Fri, 2008-08-15 at 10:52 +0800, 李日 wrote:
Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
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
actually I wouldn't worry about it. It's not cortical. Might be the optic radiation, but it will have no effect on anything you want to do. If you don't like the way it looks you could erase the wm voxels that make it up, but I wouldn't bother.
On Thu, 14 Aug 2008, Nick Schmansky wrote:
It is a defect of some kind. Use the save point / goto feature of tksurfer and tkmedit, as described in the tutorial, to see discover the cause of the defect. That is, click on a point on that needle in tksurfer, click save point, then click goto point in tkmedit, after loading the brainmask and whitematter surfaces. Probably some dura is remaining.
Nick
On Fri, 2008-08-15 at 10:52 +0800, ÿÿÿÿ wrote:
Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
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
Hello,
I'm performing a study with 10 controls to be compared with 2 groups of dementia patients, each with 10 subjects as well. I now need to create an average subject for the study, but I'm not sure if I should include the 30 subjects, only the 10 controls, or have two averages, each with 20 subjects (controls+cohort1 and controls+cohort2). What would you say is the least biased/more robust approach? Thank you!
Joao Pereira
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Bruce Fischl Sent: 15 August 2008 04:11 To: Nick Schmansky Cc: Freesurfer Mailing List; ?? Subject: Re: [Freesurfer] edit white matter
actually I wouldn't worry about it. It's not cortical. Might be the optic radiation, but it will have no effect on anything you want to do. If you don't like the way it looks you could erase the wm voxels that make it up, but I wouldn't bother.
On Thu, 14 Aug 2008, Nick Schmansky wrote:
It is a defect of some kind. Use the save point / goto feature of tksurfer and tkmedit, as described in the tutorial, to see discover the cause of the defect. That is, click on a point on that needle in tksurfer, click save point, then click goto point in tkmedit, after loading the brainmask and whitematter surfaces. Probably some dura is remaining.
Nick
On Fri, 2008-08-15 at 10:52 +0800, ÿÿÿÿ wrote:
Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
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
Hi Joao,
it depends on your goals. Note that the average subject won't affect the analysis at all, only the visualization. If you want to make inferences regarding differences in spatial location relative to the anatomy in the two analyses then you should make a single average. If they really are separate and have nothing to do with each other, then two averages would be fine.
cheers, Bruce
On Fri, 15 Aug 2008, Joao Pereira wrote:
Hello,
I'm performing a study with 10 controls to be compared with 2 groups of dementia patients, each with 10 subjects as well. I now need to create an average subject for the study, but I'm not sure if I should include the 30 subjects, only the 10 controls, or have two averages, each with 20 subjects (controls+cohort1 and controls+cohort2). What would you say is the least biased/more robust approach? Thank you!
Joao Pereira
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Bruce Fischl Sent: 15 August 2008 04:11 To: Nick Schmansky Cc: Freesurfer Mailing List; ?? Subject: Re: [Freesurfer] edit white matter
actually I wouldn't worry about it. It's not cortical. Might be the optic radiation, but it will have no effect on anything you want to do. If you don't like the way it looks you could erase the wm voxels that make it up, but I wouldn't bother.
On Thu, 14 Aug 2008, Nick Schmansky wrote:
It is a defect of some kind. Use the save point / goto feature of tksurfer and tkmedit, as described in the tutorial, to see discover the cause of the defect. That is, click on a point on that needle in tksurfer, click save point, then click goto point in tkmedit, after loading the brainmask and whitematter surfaces. Probably some dura is remaining.
Nick
On Fri, 2008-08-15 at 10:52 +0800, ÿÿÿÿ wrote:
Hi I have run the recon-all -autorecon2 command and I checked the inflate surface, it seems like something like a needle on the surface, Is this normal? I paste some pictures in the accessory, and by the way, I checked the white matter surface and pial surface and they seems all right.Can somebody tell why there is a needle on the surface? Thanks in advance.
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Joao Pereira -
Nick Schmansky -
李日