Re: [Freesurfer] Basal Ganglia in brain.mgz denoted as WM

aggressive, although it can be turned down if your sequence doesn’t have enough CNR in some regions Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of AmirHussein Abdolalizadeh Sent: Thursday, July 13, 2023 7:25 AM To: Freesurfer support list Subject: [Freesurfer] Basal

Re: [Freesurfer] Basal Ganglia Segmentation

I definitely meant to type *Dear in my email. Cheers, Maryam On Thu, Feb 11, 2016 at 2:57 PM, Syeda Wajiha Maryam wrote: > Fear Freesurfer Experts, > > I have a feeling this question has been asked already but I'm still > confused about it. Is there a way to extract the basal ganglia structure

Re: [Freesurfer] Basal Ganglia Segmentation

sure, we segment putamen, pallidum and caudate as part of the aseg.mgz (and nucleus accumbens, although that is less well-defined) On Thu, 11 Feb 2016, Syeda Wajiha Maryam wrote: > Fear Freesurfer Experts, > > I have a feeling this question has been asked already but I'm still confused > about

[Freesurfer] Basal Ganglia Segmentation

Fear Freesurfer Experts, I have a feeling this question has been asked already but I'm still confused about it. Is there a way to extract the basal ganglia structure using freesurfer? Thanks in advance for your help! Regards, Maryam ___ Freesurfer mail

Re: [Freesurfer] Basal ganglia

Hi John what parts of the basal ganglia do you want? We label caudate/putamen/pallidum/accumbens separately. You can combine them all together and get one ROI if you want. They should all be in the wmparc.mgz cheers Bruce On Mon, 21 Sep 2015, John Anderson wrote: Hi Experts, I want to do

[Freesurfer] Basal ganglia

Hi Experts, I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: precentral gyrus; ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How can I create mask for the basal ganglia ( there is no label for it). Do I need to segmenta the basal ganglia s

Re: [Freesurfer] Basal Ganglia Components

Hi Dhinakaran, 4 and 5 aren't part of our current automated segmentation. Sorry, I'm not sure how visible they are in a 1mm T1-weighted image Bruce On Wed, 17 Nov 2010, Dhinakaran Chinappen wrote: > Dear all, > > Hope your research is going smoothly. > > My question refers to the basal ganglai

[Freesurfer] Basal Ganglia Components

Dear all, Hope your research is going smoothly. My question refers to the basal ganglai components. I previously shot an email which Prof. Fischl was kind enough to reply to: the basal ganglia is not computed as a structure of its own in FreeSurfer. These are the structures of the basal ganglia

Re: [Freesurfer] Basal Ganglia

Hi Dhinakaran, we compute the volumes of structures within the basal ganglia (e.g. caudate, putamen, pallidum), which you can just add up, or analyze separately cheers, Bruce On Fri, 24 Sep 2010, Dhinakaran Chinappen wrote: > Dear all, > > I was wondering if there is a direct measurement to ge

[Freesurfer] Basal Ganglia

Dear all, I was wondering if there is a direct measurement to get the basal ganglia volume? I looked into the stats files but could get my hands on it. Is there a particular calculation to carry out? Thanks in advance, Dhinakaran Chinappen. ___ Freesurf

Re: [Freesurfer] Basal Ganglia Segmentation

Hi Paul, yes, we know this happens - it's because of the way the manual training set was constructed, so that it has voxels labeled cortex there that shouldn't exist. The accumbens in general isn't all that accurate as it has no real intensity signatures at its boundaries, so we don't use it a

Re: [Freesurfer] Basal Ganglia Segmentation

p.s. sorry, I should have looked at the images first. Everything I said still applies, but this looks worse than it should. If you put it one our filedrop I'll take a look On Wed, 24 Jan 2007, Paul Greenberg wrote: Hello, I'm having trouble getting an accurate subcortical segmentation (aseg.m