Re: [Freesurfer] Thalamus/hippocampus subfield question

Hi Victor, Being 2 separate atlases, this can happen. Maybe I should build a joint hipo/amygdala/thalamic atlas to prevent this from happening (this is why have the hippo and amygdala in the same atlas, in first place). Regarding this particular subject: if the overlap is the reflection of poor

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

External Email - Use Caution My apologies if I am missing something obvious, but isn't mri_segstats used to compute statistics on segmented volumes? I have moved my ODI map onto an inflated surface using the mri_vol2surf command, which is why I was attempting to use

[Freesurfer] Thalamus/hippocampus subfield question

?Hi, I am visually quality checking the hippocampal and the thalamic subnuclei parcellations that Iglesias designed. I see that the hippocampal tail and the PuM (pulvinar) overlay with each other. What should I make of that? Is that a brain worth removing from analysis? Victor Zeng Beth

[Freesurfer] Recon-all error

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. I successfully set up Freesurfer and I am now attempting to run

[Freesurfer] Fwd: confirm 8038f95159942b876b5e8f8110930301c8222d61

External Email - Use Caution Hi there, I really need some help…I have experienced a mild/moderate head injury in 1997 which caused me to go into seizures (no family history of epilepsy) I have had MRI recently done as my cognitive function and memory have declined rapidly

Re: [Freesurfer] Processing MRI help

External Email - Use Caution After subscribing to the mail list, I am re-trying this again. Best, Arunan From: "Selvarajah, Arunan" Date: Monday, May 24, 2021 at 8:38 PM To: "freesurfer@nmr.mgh.harvard.edu" Cc: Hanna Vasilevskaya Subject: Processing MRI help Hi, I am

Re: [Freesurfer] How to extract the GM and WM

Hi Aldo Usually we just run recon-all with -all instead of the individual -autorecon options. This will give you pretty much everything, including GM and WM Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Camargo, Aldo Sent: Sunday, May 23, 2021 11:25 PM To: Freesurfer

Re: [Freesurfer] How to extract the GM and WM

External Email - Use Caution Thanks a lot Bruce, Have a nice day, Aldo From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Monday, May 24, 2021 10:17 AM To: Freesurfer support list Subject: Re: [Freesurfer] How to extract the GM and WM Hi Aldo

[Freesurfer] mri_glm fit: gd2mtx method dods--C unrecoginzied

External Email - Use Caution Dear Experts, I am new to FS. I'm trying to run mri_glm fit I've created FSGD with 2 classes -responders vs non-responders to a given intervention- and 3 variables to be regressed out-according age, gender, laterality. I've made my FSGD file is made