[Freesurfer] A methodological question

Some weeks ago,I have posted here a compilation of the main papers that describe FreeSurfer implementation. I was wondering if someone has researched in comparison between FreeSurfer methodology and other ones. (For instance: doi:10.1016/j.neuroimage.2004.12.056) Best Regards PPJ -- --

[Freesurfer] labels to surface

Hi, using version 4.0.5. i want to convert the lh.Medial_wall.label found in the fsaverage label subdir into a mask which consists of 1 x v vector, with value 1 inside the mask, 0 outside the mask and v=#vertices. should i follow mri_label2vol and thereafter mri_vol2surf? i guess i am looking for

Re: [Freesurfer] labels to surface

Hi Joost, can you give us a bit more info? What do you want to do with the mask after you've created it? cheers, Bruce On Fri, 3 Oct 2008, j janssen wrote: Hi, using version 4.0.5. i want to convert the lh.Medial_wall.label found in the fsaverage label subdir into a mask which consists of

Re: [Freesurfer] labels to surface

Hi Joost, you can load the label into matlab with read_label.m and then convert it into the vector you want. Alternatively, there is a new version of mri_annotation2label (x64 below) which you can use to create a "segmentation" surface in nifti or mgz from an annotation. Then find "voxels" th

[Freesurfer] importing surfaces into neurolens

Hi! We're attempting to overlay group results (generated in neurolens) on a freesurfer-generated inflated brain (and pial surface) in neurolens. The neurolens administrators previously posted instructions on how to do so, but they have not been updated since freesurfer switched from the cor to

Re: [Freesurfer] importing surfaces into neurolens

Hi Angela, all the information that was in the COR-.info file is now in the .mgz file, so hopefully it should work. We switched a long time ago now, so I would think (hope?) Rick would have gotten around to supporting it. cheers, Bruce On Fri, 3 Oct 2008, Fenoglio, Angela J wrote: Hi!

[Freesurfer] Voxel resolution impact / skull stripping and bias correction replacement

Hello, I have a couple of questions on which I would like to have your opinion. The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortic

Re: [Freesurfer] Voxel resolution impact / skull stripping and bias correction replacement

João, Here is my opinion: I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study? I think you should avoid seeding data with skull striped by other program to the pipeline. Best Regards, PPJ 2008/10/3 J