Re: [Freesurfer] Hanging during Fix Topology

Hi Tali that's a giant defect. Almost 1/4 of the total normal surface area. Something must be seriously wrong. Check out the filled.mgz and see if the skull or cerebellum is attached to the wm. cheers Bruce On Fri, 6 Jul 2012, Tali Swisher wrote: Hi all, I'm running FreeSurfer v.4.0.5 (s

[Freesurfer] multiple correction

Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulat

Re: [Freesurfer] multiple correction

Hi, professor, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in

[Freesurfer] Hanging during Fix Topology

Hi all, I'm running FreeSurfer v.4.0.5 (see below) and it keeps hanging during the Fix Topology sequence while correcting defects. The last few lines before it's hanging are included below - any suggestions? freesurfer-Linux-rh9-stable-pub-v4.0.5 Setting up environment for FreeS

[Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c

I've posted a question about a strange behavior of mri_segstats if voxel size isn't 1 mm3 and --pv option is used. I found a reason of this problem in the source code of mri_segstats.c (release_5_1_0 branch was checked out from read-only CVS source-code repository) In mri_segstats.c the return

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

Thanks Douglas. It did work using the color table with just the included labels (I had to renumber the labels in the table) For left: 1 ctx-lh-bankssts 255 42 0 0 2 ctx-lh-caudalmiddlefrontal 255 14 0 0 3 ctx-lh-entorhinal 255 17 0 0 4 ctx-lh-paracentral 255 43 0 0 5 ctx-lh-parstriangularis 255 1

[Freesurfer] parcellations to fmri space

Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large v

Re: [Freesurfer] overlapping labels

Hi David, it's probably the last one it encounters, but they are not supposed to overlap. cheers Bruce On Thu, 5 Jul 2012, David Grayson wrote: Hi freesurfers,   Can a .annot file include labels with overlapping vertices? If not, then when using mris_label2annot, how does freesurfer decid