Re: [Freesurfer] longitudinal base error

Hello, Martin, I checked the norm.mgz of these two time points, nothing is wrong. Maybe I can try the new version of mri_robust_register and ...template, I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008. But it looks like this problem was unsolved.

Re: [Freesurfer] longitudinal base error

I mean to check the norm.mgz in the base. On 29.10.2010, at 09:44, Guang Zeng wrote: > Hello, Martin, > > I checked the norm.mgz of these two time points, nothing is wrong. > Maybe I can try the new version of mri_robust_register and ...template, > > I checked the mailing list. Actually, s

[Freesurfer] 3 button mouse for macintosh

Hello, Just getting started with Freesurfer. I'm hoping someone can recommend a 3-button mouse that works well with Freesurfer, on a Macintosh. I purchased a Logitech wireless mouse, but can't get it to work properly. Freesurfer does not seem to recognize the 2nd and 3rd buttons as any differ

Re: [Freesurfer] 3 button mouse for macintosh

one thing to try is to open the X11 Preferences, and look for the mouse settings, and select 'emulate three button mouse'. not the as having a three button mouse, but its an alternative. n. On Fri, 2010-10-29 at 12:42 -0400, Rosso, Isabelle M. wrote: > Hello, > > Just getting started with Frees

Re: [Freesurfer] Source matrix with zero determinant

Hi Doug, Here's the result of mri_info: ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii INFO: using NIfTI-1 qform Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii type: nii dimensions: 256 x 256 x 1

Re: [Freesurfer] Source matrix with zero determinant

The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice. doug Lisa F. Akiyama wrote: > Hi Doug, > > Here's the result of mri_info: > > ubuntu:~> mri_info > $SUBJECTS_DIR/1433_v1/mri/ori

Re: [Freesurfer] Source matrix with zero determinant

Hi Doug, There are approximately 40~45 slices of each individual's brain, each saved as separate nifti files. I'm trying to use FreeSurfer for the Non-uniform intensity normalization and skull strip functions. So, if I edit the header of each nifti file so that the slice thickness isn't 0, recon-a

Re: [Freesurfer] Source matrix with zero determinant

You would have to take all 45 slices and put them into one volume. It won''t work slice-by-slice. It is probably the case that this won't work either as we usually use high res data. For intensity normalization, maybe it will work. doug Lisa F. Akiyama wrote: > Hi Doug, > > There are approxima

Re: [Freesurfer] Source matrix with zero determinant

Hi Doug, Thanks for the tips. I will look into putting all the slices into one volume. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing

Re: [Freesurfer] Total GM and WM volumes

Hi Ed, I can't replicate this. Can you double check your numbers again? In particular, can you compare them against numbers that are printed in the recon-all.log file? In recon-all.log, look for the lines Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTo