[Freesurfer] TRACULA trac-all speed

I am currently using the last stable version freesurfer 6.0 I gave TRACULA a try on one subject and it took more that 2.5 days to finish the steps, with PC specs: - Processor core i7 4 GHz - VGA Nvidia GTX 980 with 1500 CUDA cores - 16 GB RAM I tried to speed it up (trac-all command) using

Re: [Freesurfer] Mean diffusivity on cortex?

Thank you both. How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea. Best Wishes,Shane On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia wrote:

Re: [Freesurfer] Mean diffusivity on cortex?

I'll let Doug chime in on that tool. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofi...@yahoo.com] Sent: Saturday, August 12, 2017 6:54 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] TRACULA trac-all speed

Hi Mina - The part that takes long is running bedpost. If you run trac-all with the -jobs flag, it'll write out a text file with command lines that can be run in parallel. https://surfer.nmr.mgh.harvard.edu/fswiki//trac-all#Parallelprocessing I do have long-term plans for not using bedpost, but

Re: [Freesurfer] Mean diffusivity on cortex?

Hi Shane we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out. cheers Bruce On Sat, 12 Aug 2017, Shane Schofield wrote: Thank you both. How can

[Freesurfer] Custom intensities in aparc+aseg

Dear all, I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say, 10 - ventricles, 20 - amygdala, 30 - putamen, ... I would appreciate advice on how I could achieve that. Thanks in advance, Martin

Re: [Freesurfer] Custom intensities in aparc+aseg

you mean instead of colors? I guess it would be easy enough to do in matlab. Read in the aseg, use find to find the indices of all the voxels with a particular label, then replace the label with whatever intensity you want. cheers Bruce On Sat, 12 Aug 2017, Martin Kavec wrote: > Dear all, >

[Freesurfer] Question about global mean cortical thickness

Dear FS experts: I am writting to ask for help about the computation of global mean thickness. On the FAQ page, one suggestion is that the global mean thickness is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / (lh.surfarea+rh.surfarea). I am wondering how the