[Freesurfer] delineating gyral boundaries in native space

External Email - Use Caution Hi, Is there a tool within freesurfer that can be used to delineate gyral boundaries (delineate sulci) from an individual's T1 scan in native space? To be clear, the purpose wouldn't be to broadly identify or parcellate different gyri, but to

[Freesurfer] Intensity equalization

External Email - Use Caution Hi, I have 2 MRIs on different scanners. The tissue contrasts are slightly off and there is slight differences in the volumes of ROIs. Is there a way to make both MRIs have the same intensity? I.e., Im2's intensity follows Im1's intensity? Many thanks

[Freesurfer] Total WM surface area

External Email - Use Caution Hi, Are the total lh/rh cortical surface areas in stats/aparc.stats = parcel1 surface area + parcel2 surface area…? Get Outlook for

Re: [Freesurfer] sbTIV versus eTIV

External Email - Use Caution Many thanks. Best On Tue, Jul 20, 2021, 14:36 Douglas N. Greve wrote: > The two methods are totally different. See >

Re: [Freesurfer] sbTIV versus eTIV

The two methods are totally different. See https://surfer.nmr.mgh.harvard.edu/fswiki/sbTIV the sb version actually performs a skull segmentation  and counts voxels within skull. The eTIV is computed from the talairach registration, which is going to be inherently more variable (eg, more or less

[Freesurfer] sbTIV versus eTIV

External Email - Use Caution Hi, I am looking at interscanner differences between Philip and GE. I get significantly less variation between the scanners when looking at sbTIV (coefficient of variation < 1.5 %) than eTIV (12%) within subjects. Any thought as to why?

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported  About the second issue, was there something in your config file about where to find the training data, or did you just use the default? Thanks, Anastasia.

[Freesurfer] DOSS Question

External Email - Use Caution Dear FreeSurfer Experts, I have been having trouble with performing DOSS analyses with mri_glmfit. One of the groups in my sample is too small to be performed with DODS, but when I try to call the DOSS option in mri_glmfit, it returns the same error,

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

External Email - Use Caution Hi Anastasia, I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually: - I did thalamic segmentation using the T2 beside the T1 sequence, thus

Re: [Freesurfer] Developer password

External Email - Use Caution Hello, I am also in need of the developer password for running freesurfer through VirtualBox. Is it possible to get the info sent to my email? Thank you, Eli From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf

[Freesurfer] Announcing the new version of TRACULA, included in FreeSurfer 7.2

Hi all - After a year of lockdown coding, and a couple more years of tireless work by the tract annotation team, we are pleased to share the new version of TRACULA. For a summary of new features see: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Of note, new protocols were developed

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution The default path you show me is exactly what I want! Thank you! Kiyotaka On Tue, Jul 20, 2021 at 8:23 PM fsbuild wrote: > While it does not currently work to change the default install path, that > default install path for the .deb (and .rpm) 7.2.0

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution While it does not currently work to change the default install path, that default install path for the .deb (and .rpm) 7.2.0 installer files is /usr/local/freesurfer/7.2.0 (which reads like the path you want to use). If you already have different

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution Hello R, Thank you for letting me know that the deb file is now available. It's so useful for Ubuntu users to install FreeSurfer using the deb file. Can I ask you one more question? Can I specify the install directory using the deb file? I manage

Re: [Freesurfer] MNI to RAS conversion

External Email - Use Caution That would be 8b on that wiki page. Maybe the Yeo Registration fusion approach is also interesting for you, see

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution Hello Kiyotaka, You may not need to be concerned about that warning. You can suppress it by setting the following in your shell environment. $ export NO_MINC=1 For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the

[Freesurfer] MNI to RAS conversion

External Email - Use Caution Dear Mailing List, I have a set of MNI coordinates (from SPM2) that I need to visualise relative to the Desikan-Killiany Atlas parcellation. However, I'm unsure how to convert these coordinates so that I can load up Freeview and visualise their