[Freesurfer] detecting movement artifact

Hello, freesurfer experts We are doing the structure scan on the adolescents. One potential problem is the head movement from the participants. But so far from the image, it looks ok. The question is 1 What is the visual check after autorecon3? We did the visual check after autorecon1 a

Re: [Freesurfer] detecting movement artifact

after autorecon3 look at the two .annot files and see if they seem accurate. If so, then the spherical morph worked. cheers, Bruce On Mon, 13 Apr 2009, karlkarl wrote: Hello, freesurfer experts We are doing the structure scan on the adolescents. One potential problem is the head movement

[Freesurfer] total brain volumes

I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know. -Original Message- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/200

Re: [Freesurfer] total brain volumes

Hi Nate, sorry, I think we were each waiting for someone else to answer :). I'm not sure about the BrainSegVol. It shouldn't include ventricle in principle, but in practice it might. Probably the easiest thing to do is to use mri_label_volume -a aseg.mgz which will give you the volume of all

Re: [Freesurfer] total brain volumes

Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button. doug Dankner, Nathan (NIH/NIMH) [F] wrote: I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been an

RE: [Freesurfer] total brain volumes

I've checked out the wiki, and it brings up a couple of other questions. I don't seem to have the BrainSegVolNoVent measure...maybe this is an issue with versions? I ran the mri_label_volume command that Bruce provided. There was roughly a 300,000 mm^3 difference between the output of the mri

Re: [Freesurfer] total brain volumes

Not having BrainSegVolNoVent might just mean that you have an old version. It was added two years ago, but I'm not sure which build that would have gotten into. Not sure about the discrepancy with mri_label_volume. doug Dankner, Nathan (NIH/NIMH) [F] wrote: I've checked out the wiki, and it

Re: [Freesurfer] total brain volumes

probably partial volume correction, which is a good thing to do. On Mon, 13 Apr 2009, Douglas N Greve wrote: Not having BrainSegVolNoVent might just mean that you have an old version. It was added two years ago, but I'm not sure which build that would have gotten into. Not sure about the disc

RE: [Freesurfer] total brain volumes

Ok, sorry to be a bother, but I just want to be sure I'm getting accurate volumes here. Using the mri_label_volume method on one particular scan, the output volume is 500,000 mm^3 less than that of BrainSegVolNotVent (which is approx 1.2 million mm^3). Bruce, I know you mentioned that this is

[Freesurfer] mni152.register.dat

Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal ___ Freesurfer mailing list Fre

Re: [Freesurfer] mni152.register.dat

you don't need to invert it, just use as is. doug Yigal Agam wrote: Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal