Re: [Freesurfer] Temporal lobes not included

Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects. doug On 2/8/13 5:56 PM, Bruce Fischl wrote: Hi Kristina I would guess you have a topological defect that is being fixed inco

Re: [Freesurfer] Multi-voxel pattern analysis

Hi all, is this tool going to be available to download with the 5.2? I am interested in it too. thanks! Gari On Thu, Feb 7, 2013 at 3:09 AM, Bruce Fischl wrote: > Hi Luisa > > yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm > called RvoxM that I believe is state-of-the-art

Re: [Freesurfer] surface morphology

Hi Fred we have done some of this, but the tools for doing so aren't documnted or streamlined like recon-all. Localizing is a bit dicey as the apparent localization may have more to do with the regularization in your 3D warping than anything else. Martin Reuter has some interesting tools for q

Re: [Freesurfer] Temporal lobes not included

Hi Kristina I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling) Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote: Hello,     I am trying to run cortical thickness on a few scans.

[Freesurfer] the mid point slide bar doesn't come back to 0 by manually entering 0 in the freeview

Hi freesurfer experts, I'm a newbie for the free surfer and am playing around with the freeview GUI. I'm having trouble moving the slide bar back to '0' by manually entering '0' right next to the Mid point slide. Interestingly, the slide bar moves when I entered other values like -2 or 2, but it d

[Freesurfer] surface morphology

Hi All, Is there an approach within freesurfer (or related software) for examining surface morphology of subcortical structures? WIth freesurfer I'm able to examine the total volume of various subcortical structures, but if my participants differ in volume of a subcortical structure, I can't dete

Re: [Freesurfer] mrisReadTriangleFile failed

Also note that there are "IsRunning" files created in the scripts folder. If those still exist, then it will come back saying to delete them first. doug On 2/8/13 3:13 PM, Bruce Fischl wrote: > so they might have finished properly if you hadn't done so? Try running > -make all again. In theory

Re: [Freesurfer] mrisReadTriangleFile failed

so they might have finished properly if you hadn't done so? Try running -make all again. In theory it's only supposed to reru what is needed. Bruce On Fri, 8 Feb 2013, Jonathan Holt wrote: > No, the computers they were running on had to be rebooted before they > finished. > On Feb 8, 2013, at

Re: [Freesurfer] mrisReadTriangleFile failed

No, the computers they were running on had to be rebooted before they finished. On Feb 8, 2013, at 1:19 PM, Jonathan Holt wrote: > Basically, I had a bunch of recon-all's terminate without finishing. Do I > need to run recon-all -s -make all, or can I run as usual? > > jon > On Feb 6, 2013, at

Re: [Freesurfer] mrisReadTriangleFile failed

do you mean they finished with an error? If so, what was it? On Fri, 8 Feb 2013, Jonathan Holt wrote: > Basically, I had a bunch of recon-all's terminate without finishing. Do I > need to run recon-all -s -make all, or can I run as usual? > > jon > On Feb 6, 2013, at 9:35 PM, Jonathan Holt wrot

Re: [Freesurfer] mrisReadTriangleFile failed

Basically, I had a bunch of recon-all's terminate without finishing. Do I need to run recon-all -s -make all, or can I run as usual? jon On Feb 6, 2013, at 9:35 PM, Jonathan Holt wrote: > Just had a cluster of computers lock up, unfortunately resulting in several > freesurfer jobs terminating

Re: [Freesurfer] Large differences in subcortical structure volume between native and FreeSurfer space

Hi Sean, there are two possibilities. First, FS includes partial volume correction when estimating the size of hippocampus (and the other subcortical structures). Second, if you take it from a 1mm3 space to a space with larger voxels, then many voxels in the edge will be indeterminant, and th

[Freesurfer] Large differences in subcortical structure volume between native and FreeSurfer space

Dear experts, I would like to ask for help in explaining an unexpected difference in volume in subcortical structures between orig.mgz space and rawavg.mgz space scans. I used FreeSurfer (v5.1, Mac 10.7.5) on a group of subjects in order to extract subcortical segmentation volumes. I then changed

[Freesurfer] public MRI dataset, alzheimer's and controls, MIRIAD

Dear FreeSurfer users, We are happy to announce the release of a new publicly available dataset of volumetric brain MRI of Alzheimer's patients and age-matched controls: MIRIAD (Minimal Interval Resonance Imaging in Alzheimer's Disease). MIRIAD complements existing datasets such as ADNI by prov

[Freesurfer] Pixels left after manual correction of subcortical regions.

Dear FreeSurfer, When i manually have corrected some areas of subcortical structures (ex Caudate) i still get some pixels left of other regions (NAcc for ex) in the corrected area after I again have run recon-all -autorecon2 and -autorecon3. It seems like the program does not read my alteration