[Freesurfer] making the face mask thicker mideface

External Email - Use Caution Is there a way to make the face mask generated by mideface thicker? On its own it is fine however when we need to deface a T2 there may be some motion such that the mask does not do well when registered to the T2. ___

[Freesurfer] Inconsistency between mean cluster cortical thickness value and lme_lowessPlot

External Email - Use Caution I've been performing a LME longitudinal analysis on a dataset with two groups (controls, clinicals), where each participant completed two MRI scans (pre, post). I was examining a particular surface cluster that arose from a time*group interaction effec

[Freesurfer] Hypothalamic region segmentation

External Email - Use Caution Dear the Freesurfer community, I am trying to segment the sub-ROIs of the hypothalamus using the mri_segment_hypothalamic_subunits tool, but I keep getting an error that says "zsh: illegal hardware instruction." I ran the recon-all command first and th

[Freesurfer] mideface: facemask not found

External Email - Use Caution I have been writing scripts with the mideface program. Her the exact line of code i am using. mideface --i $Anatfolder/${mprs[0]}_T1w.nii.gz --odir $defacefolder --o $defacefolder/bids/${mprs[0]}_desc-defaced_T1w.nii.gz --pics --facemask facemask.mgz

Re: [Freesurfer] Hypothalamic region segmentation

External Email - Use Caution  Hello Raphaela, You probably installed the Intel Mac binaries to run on your Silicon Mac with an M1, M2, or M3 arm64 chip.  But not all Intel code will run on the newer arm64 Macs.   You instead need to download and install the Silicon Mac nightly f