Re: [Freesurfer] Entorhinal Labels and labels generally

Hi Joshua the labels are surface based and by default are shown on the ?h.white surface, giving the appearance you noted. You can use mri_label2vol to sample them into the volume and for example fill the ribbon if you want, but since each point on the surface has an associate thickness value,

[Freesurfer] Entorhinal Labels and labels generally

I'm relatively new to Freesurfer, and have mostly focused of the aseg.mgz segmentation. However, I am also interested in entorhinal cortex and loaded the label up in tkmedit. What I noticed was that it seemed each label essentially noted the border between white and gray matter, but didn't really c

Re: [Freesurfer] generate binary mask from GLM output

You can use mri_binarize, something like mri_binarize --i sig.mgh --min 3 --o mask.mgh Note that sig.mgh is a signed quantity. If you want it unsigned, then use --abs above doug Miranka Wirth wrote: > Dear Freesurfers, > > I would to like to generate a binary surface-based mask from the GLM

[Freesurfer] generate binary mask from GLM output

Dear Freesurfers, I would to like to generate a binary surface-based mask from the GLM output file (e.g., sig.mgh) the way that vertices above a certain p threshold are set to 1 and below this threshold to 0. I believe I can use this mask in the mri_glmfit procedure? Thank you for helpful inform

Re: [Freesurfer] Tracula - bedpost failure

Hi Kiely, I had a similar experience with one of my subjects, but I realized that the original diffusion image had a lot of signal loss in various regions and hence the subsequent registration steps failed. It can happen when either intra-subject or inter-subject registration fails. I would inspe

Re: [Freesurfer] Tracula - bedpost failure

Hi Anastasia, Sorry for my slow reply. I am working with data that I only have access to intermittently. We were able to fix the problem by deleting the original files from the folder and re-running the bedpost step. The old files must have been interfering in some way. I am hoping you can help m

Re: [Freesurfer] building a pipeline using mri_robust_register and other FS functions

Hi Mehul why not just run the longitudinal stream, then subtract the longitudinal results? I would probably look at the subtraction of the norm.mgz. cheers Bruce On Tue, 24 Jan 2012, Mehul Sampat wrote: Hi Folks,We have subjects with high lesion load which changes significantly over time. 

Re: [Freesurfer] Extracting Cortical Thickness for Parcellated Data

No, that's not needed, otherwise you would be blurring your parcellation boundaries. Best, Martijn On Tue, Jan 24, 2012 at 6:37 PM, Jeff Stout wrote: > Hi All, > I am relatively new to freesurfer. I am trying to extract cortical > thickness information from the freesurfer data. What is the di

[Freesurfer] building a pipeline using mri_robust_register and other FS functions

Hi Folks, We have subjects with high lesion load which changes significantly over time. I want to use FS functions to build a pipeline for comparing lesion changes in two time-points of the same-subject. I am thinking of using the following steps; 1) Use mri_normalize to normalize the two time-poi

[Freesurfer] Extracting Cortical Thickness for Parcellated Data

Hi All,I am relatively new to freesurfer.  I am trying to extract cortical thickness information from the freesurfer data.  What is the difference (with thickness options as outputs) between asegstats2table and mris_anatomical_stats.  I see that asegstats2table gives the option for multiple Sub

Re: [Freesurfer] mri_glm with grf over CVS space

Hi Doug, Many thanks for your help. I have one more questions please. You were telling me that: "Given that FA is very non-gaussian, a lot of people prefer to use permutation". What this means? Do I need to run something different than: mri_glmfit-sim \  --glmdir Group_Analysis.glmdir \  --gr

[Freesurfer] hippocampal subfield segmentation

Dear Van Leemput & Freesurfers, I've been working with the GEMS tool for hippocampal subfields segmentation and have a question I would like to ask you. I've noticed that the CA1 sector appears to be quite small compared to other subfields (CA2-3 seems to be the largest), while previous studies s

[Freesurfer] recon-all -use-gpu issue

Hi everybody, I am trying to use recon-all with gpu. So I installed the CUDA librairies successfully (it seems). I am using freesurfer 5.0, cuda driver 3.2. Here is the cudadetect output : Detecting CUDA... There is 1 device supporting CUDA: Device 0: "D13U" CUDA Driver Version: