[Freesurfer] white matter snr

Hi, I would like to know whether it is a good idea to use the snr measure from *wm-anat-snr *as a covariate in lme (or glm) analyses? I find significant effects of snr on cortical area and thickness. Am I right in thinking I should be more cautious about interpreting findings in regions where wm s

Re: [Freesurfer] Speeding Freesurfer

> My impression is that CUDA drivers are not available for AMD FirePro > graphics boards. Aren't they? Sorry, I dont know the answer to that question. In regard to the next release of freesurfer, my guestimate would be between 1-2 months. -Zeke On 12/03/2014 02:12 AM, Francesco Cardinale wro

Re: [Freesurfer] Speeding Freesurfer

CUDA is specific to NVIDIA graphics devices. http://www.nvidia.com/object/cuda_home_new.html On Thu, Dec 4, 2014 at 10:10 AM, Z K wrote: > > My impression is that CUDA drivers are not available for AMD FirePro > > graphics boards. Aren't they? > > Sorry, I dont know the answer to that question

[Freesurfer] --pca flag on mri_glmfit

Dear Freesurfer experts, Potentially super-noob question here, but I'm curious about the --pca flag on mri_glmfit. I can see that it does PCA/SVD on the dataset? in question and saves the residuals to the glmdir specified, but I was unable to find anything in the documentation describing what exa

[Freesurfer] Some questions about fsaverage

Hello, I am currently working with cortical thickness and more particularly with the fsaverage. Since the thickness has the same number of voxel, I would like to correspond the voxels with some ROI, for instance the Desikan-Killiany Atlas

Re: [Freesurfer] Some questions about fsaverage

you can use mri_annotation2label to convert each annotation into a label. The label is a text file with a list of indices. doug On 12/04/2014 02:25 PM, Alexandre Routier wrote: > Hello, > > I am currently working with cortical thickness and more particularly > with the fsaverage. Since the thick

Re: [Freesurfer] --pca flag on mri_glmfit

It performs pca/svd on the residuals. The sdiag.mat I think includes the singular values but also the percent variance explained by each component and the cumulative explained by all components upto and including that component. You probably just need to change the overlay thresholds on the v.

Re: [Freesurfer] mri_surfcluster problem

It cannot read the .w file as input. There is no need to use .w files (despite what it might say). On 12/03/2014 12:22 AM, wangzhiwei3233 wrote: > *The command I used is* /mri_surfcluster --in sig.w --subject > fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum > area100.pos.cluste

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ >From that help and your email I'm loo

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

Sorry - if anyone's looking at this in the future, you also need --regheader in the command: mri_vol2surf --mov \ --o $ \ --projdist -2 \ --interp nearest \ --surf pial \

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

Yes doug On 12/04/2014 03:41 PM, Kirstie Whitaker wrote: > Thank you, Doug. > > Can I just check that projdist is the same as projabs but with a > different name? > > Just in case I'm using an old/wrong version, here's the last line from > the mri_vol2surf help output: > $Id: mri_vol2surf.c,v 1

Re: [Freesurfer] Some questions about fsaverage

Hi Alexandre I'm not entirely sure what you are asking, but the fsaverage Brodmann areas and parcellations should all be stored in the directory: $FREESURFER_HOME/subjects/fsaverage/label cheers Bruce On Thu, 4 Dec 2014, Alexandre Routier wrote: Hello, I am currently working with corti