Re: [Freesurfer] white.surf doesn't follow wm.mgz

then you didn't fix it properly. Did you find the source of the defect? This is kind of an acquired skill as you have to page through a number of slices almost by definition, and sometimes need to look in different orientations. If you point us at the data (and the voxel coords of the problem)

Re: [Freesurfer] Count non-zero voxels without matlab

mri_label_volume -a brain.mgz should do the trick. cheers, Bruce On Mon, 22 Sep 2008, Jeff Sadino wrote: Hello surfers, I would like to count the number of non-zero voxels in the image brain.mgz. Does anybody have any ideas what the easiest way to do this would be without using matlab? T

Re: [Freesurfer] white.surf doesn't follow wm.mgz

Thanks Bruce. But what happens when I've already done the manual edit, run autorecon2-wm and still see the defect? > Hi Dahlia, > this usually means there was a topological defect that was fixed > incorrectly. You'll need to edit the wm.mgz to remove it, then run > autorecon2-wm. > > cheers, > Bru

[Freesurfer] Count non-zero voxels without matlab

Hello surfers, I would like to count the number of non-zero voxels in the image brain.mgz. Does anybody have any ideas what the easiest way to do this would be without using matlab? Thank you all! Jeff Sadino _ Want to do more w

Re: [Freesurfer] white.surf doesn't follow wm.mgz

Hi Dahlia, this usually means there was a topological defect that was fixed incorrectly. You'll need to edit the wm.mgz to remove it, then run autorecon2-wm. cheers, Bruce On Mon, 22 Sep 2008 [EMAIL PROTECTED] wrote: Hi, What should I do when the white volume looks right (e.g. filled in w

Re: [Freesurfer] Spherical visualization

I just want to make an illustration like the figure 6 or figure 7 from your 99 paper in Neuroimage. Thanks PPJ 2008/9/22 Bruce Fischl <[EMAIL PROTECTED]> > Hi Pedro Paulo, > > can you clarify what you mean? Do you want to visualize the individual > subject thickness map on it's spherical map? Th

[Freesurfer] white.surf doesn't follow wm.mgz

Hi, What should I do when the white volume looks right (e.g. filled in where needed) but the white surface doesn't follow the boundary of the volume? I've done recon-all with autorecon2-wm and autorecon3. Thanks! Dahlia. ___ Freesurfer mailing list Free

Re: [Freesurfer] Spherical visualization

Hi Pedro Paulo, can you clarify what you mean? Do you want to visualize the individual subject thickness map on it's spherical map? That would be: tksurfer $subject $hemi sphere.reg -overlay $SUBJECTS_DIR/$subject/surf/$hemi.thickness cheers, Bruce On Mon, 22 Sep 2008, Pedro Paulo de Magalh

[Freesurfer] Spherical visualization

Sorry for the question but in order to generate the visualization of the spherical mapping of, for instance, cortical thickness we should use which command line in TKSurfer? -- --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfi

Re: [Freesurfer] fsaverage across versions

Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the regi

[Freesurfer] fsaverage across versions

Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverag

Re: [Freesurfer] Methodology Papers.

back from vacation. Thanks ever so much for this Pedro. It will keep me on track. Pedro Paulo de Magalhães Oliveira Junior wrote: Matt, I have a table I use sometimes. It contains 12 references I believe are the most important and their role in recon-all process. Regards, PPJ 2008/9/12