[Freesurfer] password for 7z OVA file

External Email - Use Caution Hi everyone, I’d like to receive the password for the 7z ova file please. The file i have is FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you, Andre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error

External Email - Use Caution Hi Yujing,   Thank you very much for clarifying and letting me know of your testing results.  I really appreciate all your help with this issue. Andrew *Andrew Beaudin, PhD* | Research Associate University of Calgary | Cumming School of

Re: [Freesurfer] FS FAST

External Email - Use Caution Hi all, I'm trying to run preproc-sess on a resting state MRI and I've tried to define python to python3 path. I assume it's trying to call python into the environment but I'm not sure how to do this. I'm running a macOS m1 apple chip. I've tried

[Freesurfer] Virtual Machine password

External Email - Use Caution Hello! I would like to try FreeSurfer on VM, but I need the password for archive. I hope that this is the right place to ask for it. (I can't find other e-mail address). Many thanks! ___ Freesurfer

Re: [Freesurfer] T2pial: Numerical argument out of domain

Hi Amir, Thanks for the update. I don’t have answer for you. I’m just curious if you tried Freesurfer 7.2 and what is the outcome. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of AmirHussein Abdolalizadeh Sent: Tuesday, February 7, 2023 9:16 AM To: Freesurfer support

Re: [Freesurfer] Help with script with 7.2 on an HPC

Hi Lisa, You can find information about those scripts here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Executing the corresponding script with the flag -help should provide some information too. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error

Hi Andrew, I have added an option ‘--frobnorm-thresh <>’ to mri_robust_template in Freesurfer dev branch. It can be used to set threshold for MyMatrix::RotationMean(). The default is 0.0001. Increasing the threshold didn’t help when I tested it with your data. The change is not in release

Re: [Freesurfer] T2pial: Numerical argument out of domain

External Email - Use Caution Hi again, An update: Repeating the analysis using 7.1.0 ends without any errors. Visually checking the results also seems totally fine. I think it is something specific to 7.3.2. Of note, my subjects are elderly with variable degrees of white matter

Re: [Freesurfer] MRI image quality metrics

Hi, The following is taken from https://github.com/ComaRecoveryLab/Lesion_Correction as mentioned in this paper https://www.sciencedirect.com/science/article/pii/S2215016120302144 “ Qualitative and Quantitative Assessment of MRI Data SNR: We calculated SNR for each subject using the

[Freesurfer] creating a freesurfer guix package definition (aka compiling from source)

External Email - Use Caution Hi, I'm trying to create a freesurfer (v7.3.3) package definition for guix. I have some problems during freesurfers configure step though. I'm using the following definitions to build freesurfer (this may not help much if you don't know guix, but

[Freesurfer] MRI image quality metrics

External Email - Use Caution Dear FreeSurfer experts, Please, I need your assistance and guidance on calculating the contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White matter, Gray matter, and CSF of the brain after recon-all. Thank you