[Freesurfer] ROI from left to right hemi - cortical thickness

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I

[Freesurfer] mris_divide_parcellation

Dear all, I'm using mris_divide_parcellation to subdivide cortical regions into smaller regions and I've some questions about such process. I would like to transform my new annot file to labelled surface and labelled cortical volume. For the former, there's a 'simple' way to transform annot file

[Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

Hello, since I experienced a high rate of registration errors using talairach_avi in the conventional recon-all processing stream (more than 50% misregistration), I would like to incorporate SPM affine registration parameters (as provided in the seg_inv_sn.mat file obtained from the segmentatio

[Freesurfer] Brainhack 2012

Dear colleagues, I wanted to draw your attention on the upcoming 2012 Brainhack, 1st edition, to be held from September 1-4 at the Max Plank Institute for Human Cognitive and Brain Sciences, Leipzig, Germany. Brainhack is not a conference or a workshop. It should be closer to one of those exciting

Re: [Freesurfer] wm problems

Hi Nicole what version are you running? It's hard to diagnose from just the images. In general, if the surface doesn't follow the wm.mgz it means there was a topological defect that was corrected in that region. You can find it and fix it be editing the wm. If you can't find it, upload it and

Re: [Freesurfer] wm problems

Hi Bruce, It's version 5.1. Thanks for the suggestion about the second problem (surface not following wm). For the white matter hypointensity problem (surface follows wm volume, but wm is incorrect; this occurs in several places on multiple subjects), will we just have to delete this manually from

Re: [Freesurfer] wm problems

Hi Nicole I saw this before and couldn't replicate it. Sure, upload an example and I'll take a look. Hopefully it is something that is resolved in 5.2. Bruce On Mon, 9 Jul 2012, Nicole Senecal wrote: Hi Bruce, It's version 5.1. Thanks for the suggestion about the second problem (surface not

Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

Hi Simon what version are you using? Avi Snyder (ccd) has been tracking down some interactions between his talairach code and our intensity normalization that seem to have made it more fragilie, particularly in 5.1. He has some suggested fixes that may improve things for you. cheers Bruce

Re: [Freesurfer] nu_correct problem

I believe this post slipped through the cracks. Anyone have any thoughts on this nu_correct error. Some subjects ran fine, so it seems to be an intermittent problem and not an installation problem. Also, is this possibly related to the avi_talairach/intensity normalization issues being discussed i

[Freesurfer] multiple correction

Hi, freesurfer expert, I have three questions about the multiple correction. 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