[Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

External Email - Use Caution Hello FreeSurfer Developers, First, I am new to using Freesurfer, so I apologize if any information is unclear. I am attempting to use the following tutorial https://secure-web.cisco.com/1KKgvfrXJGjQJ5zjq_uJgVI7FZF_1Yms747_s_N5YKZgNCGOMeS-uBP8-XyfvG

[Freesurfer] Basic question

External Email - Use Caution Dear Freesurfer team, I know this is a basic question, but I would like to be sure before proceeding. Are those statements below right? For cortical thickness, I should covariate for age and sex For volume, I should covariate only for TBV Thank you

Re: [Freesurfer] Basic question

Hi Rosie It really depends on what your hypotheses are, but if you are covarying for age and gender in thickness you probably want to do so in an analysis of volume as well. The only real difference are (1) thickness doesn’t really need TBV covariation, and (2) thickness is a more localizable q

Re: [Freesurfer] Basic question

External Email - Use Caution Hi Bruce, Thank you very much for your answer. Kind regards, Rosie On Sun, Nov 21, 2021 at 8:04 PM Fischl, Bruce wrote: > Hi Rosie > > > > It really depends on what your hypotheses are, but if you are covarying > for age and gender in thickness

Re: [Freesurfer] TRACULA configuration file for bash

Hi Luis - Not sure if you've tried this already, but the instructions on the wiki should work regardless of what your default shell is, because trac-all will source the configuration file from within a c shell. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Tracula 7.2 using older structural outputs

Hi Jim and Luis - The only change between versions of recon-all that would mess things up for TRACULA would be if the IDs of the structures in the aparc+aseg changed (e.g., the left thalamus changed from 10 to 100) or a new structure got added to the aparc+aseg that wasn't there in the previous

[Freesurfer] Requesting to clarify doubts on data analysis

External Email - Use Caution Dear FreeSurfer team, I have a few questions to clarify the confusion regarding data analysis. 1. For each subject, is it recommended to normalize the raw volumetric data by total intracranial volume? If so, is it true only for volumes of sub

Re: [Freesurfer] Pipeline errors - matlab

External Email - Use Caution Hello Eugenio, Thank you so much for your response. Here is a large section of the error message I got while running hippocampal subfields. Please let me know if more details are needed! *--

Re: [Freesurfer] Pipeline errors - matlab

External Email - Use Caution The Matlab MCRv84 release used by Freesurfer is too old to be supported on MacOS 11 Big Sur by The Mathworks (looks like you are running MacOS 11.5 beta 2 release). There are also error reports similar to yours with old versions of Matlab on differen