[Freesurfer] read in .vtk files ?

Hello All, Can freesurfer read in .vtk surface files ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Three classes and GLM

Hi all, I'm having some problems getting a second level fixed effects analysis started on my subjects. There are three runs (dofsum = 884) in each case I'd like to compare. OSGM works fine so far, but when I apply a matrix like this: 1 0 0 0 1 0 0 0 1 To a contrast like that: 0.5 0.5 -1 mri_g

Re: [Freesurfer] follow-up to Hausdorff distance question

it should be with the current version. If you tell us what hardware/software platform you are using we can send you a version Bruce On Thu, 16 Jul 2009, Jared Price wrote: Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that

[Freesurfer] follow-up to Hausdorff distance question

Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that could calculate it, but I don't see it in the /Applications/freesurfer/bin directory. Is it elsewhere? Is it included with 4.4.0? ___

RE: [Freesurfer] ANOVA and co-variable

Thank you so much for you response! I will submit a bug following the rule. However, I do think it is not a bug but a statistic misunderstand. The root of this problem is the variable C in two classes (e.g., A1B1 and A2B1) are all Zeros. If I add one non-zero number in C in these two classes, ever

Re: [Freesurfer] mean symmetric surface distance, Hausdorff distance etc..

Hi Jared, yes, we have both volumetric and surface-based: mris_hausdorff_dist usage: mris_hausdorff_dist [options] -a compute pairwise HD between all annotations mri_hausdorff_dist USAGE: mri_hausdorff_dist... where options are: -b binarize input volum

[Freesurfer] mean symmetric surface distance, Hausdorff distance etc..

Hi freesurfer masters, I was wondering if freesurfer had a way of comparing two segmentations for surface differences, something along the lines of a Hausdorff distance or the symmetric mean absolute surface distance Cheers, Jared ___ Freesurfer maili

Re: [Freesurfer] running freesurfer after talairach touch-ups...

After fixing the Talairach registration, you need to rerun the whole recon-all process. The old files will be overwritten. recon-all -all -s And after adding control points, you need to run, recon-all -autorecon2-cp -autorecon3 -s Sita. On Thu, 16 Jul 2009, Ritobrato Datta wrote: Hel

[Freesurfer] running freesurfer after talairach touch-ups...

Hello all, I ran recon-all -autorecon-all -s After it ran all the way through, I ran tkregister2 --mgz --s --fstal --surf orig and saved everything with the SAVE REG button in the tkregister2 toolbar. Since I initially ran all the steps before the talairach touch-ups, what do I run to re

Re: [Freesurfer] ideal freesurfer input?

Hi Stephen, the TFE is probably fine, or a good quality mp-rage. My only concern with the 8 channel is how uniform the B1 field is. Do you see large drop-offs near the top of the brain? We currently don't support multi-spectral inputs for most of what we do, although we do have some prototype

[Freesurfer] Confusion about mri_label2label

Hello, I'm attempting to convert labels from one subject's cortical surface to locations or nodes on another's cortical surface via spherical registration. My thought was to use mri_label2label, e.g. mri_label2label --srcsubject Bob --srclabel Bob/label/lh.cortex.label --trgsubject bert --trglab

Re: [Freesurfer] ANOVA and co-variable

Hi Zhang, when reporting a bug or problem, please refer to the following suggestions in terms of what information you should report: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks! doug Zhang, Xiaochu (NIH/NIDA) [F] wrote: Thank you so much for your answer! Now I meet another problem.

Re: [Freesurfer] changing image orientation

Hi Jose, this is fraught with peril as you won't know left from right. What format was the data in? Ideally you would want to get access to a format that has the direction cosines. cheers Bruce On Thu, 16 Jul 2009, Jose Luis Cantero Lorente wrote: Hi there, I got some mgz files badly

[Freesurfer] changing image orientation

Hi there, I got some mgz files badly reoriented (saggital right - nose bottom, and needed them in saggital left - nose up). Would it be feasible to change the reorientation and save them to mgz from the Freesurfer command line? Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Labora

[Freesurfer] Freeview for Mac

Hi, I have a quick question: has freeview been compiled for an intel macbook pro? Thanks, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer