[Freesurfer] brain volumes normalization

External Email - Use Caution Hello freesurfers, I have some questions about the output variables of Freesurfer: 1. In the case of brain volume normalization, do I need to normalize all the volumetric results to the eTIV or just the subcortical volumes? 2. Are there any formulas ot

Re: [Freesurfer] Figures for publication

I would use either the ocn (cluster annotation) or the cluster-wise corrected map: overlay as you generally don't want to show uncorrected data. As for the max, it is a personal choice, just what you think looks good or makes your point. On 4/22/2024 7:52 AM, Asuka Toyofuku wrote: Ex

Re: [Freesurfer] brain volumes normalization

On 5/2/2024 4:03 AM, yunus soleymani wrote: External Email - Use Caution Hello freesurfers, I have some questions about the output variables of Freesurfer: 1. In the case of brain volume normalization, do I need to normalize all the volumetric results to the eTIV or just the subcor

Re: [Freesurfer] question about infantfreesurfer

Hi Knut, The version available on the freesurfer wiki is the one that corresponds to our original publication. You can use it in your publication. Lilla From: Knut J Bjuland Sent: Tuesday, April 23, 2024 4:38 AM To: freesurfer@nmr.mgh.harvard.edu ; Zollei, Lill

Re: [Freesurfer] Infant Freesufer auto-recon failure

Hi Rachel, The autorecon-pial option is not yet implemented in infant freesurfer that is why you see the below error. Best, Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lemley, Rachel Sent: Monday, April 22, 2024 3:21 PM To: Freesurfer@nmr.

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

Hi Dan, a) yes b) yes Best, Martin On 22. Apr 2024, at 17:09, Dan Levitas wrote: Hello, I've been following the FreeSurfer longitudinal LME analysis tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/f

[Freesurfer] brain volumes normalization

External Email - Use Caution Thank you for the help.my next question When I normalize the surface area to the eTV, they are in different units (mm2, mm3). The resulting unit will be 1/m, is that okay? ---

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hi Martin, Thanks for the response! After my original post I went through things more carefully based on my two original two questions and made a follow-up post here (https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-mDFOvCAyWs2k

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

Hi Dan, I have not worked with this code in a decade, but Kersten in my group maintains our R package of it ( see https://github.com/deep-mi/fslmer ). I will bring this to his attention. Basically I think you determine the joint p-threshold across hemispheres and convert it to FreeSurfer ( -

[Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

External Email - Use Caution Hi FS support team, I am going to be using mri_glmfit to test 1) main effects (which regions show differences in cortical thickness between group 1 and group 2) and 2) interaction effects (does the relationship between IV and DV depend on moderator). D