[Freesurfer] Subcortical surfaces from volume features.

External Email - Use Caution Dear Freesurfer Experts, I am looking into generating subcortical surfaces from the subcortical volumes generated from recon-all. The reason for this is I am trying to create a vertex based Morphological Similarity Network generated from both

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

External Email - Use Caution Thank you Douglas. That’s much clearer. I do however, have a subject without a gender disclosure. Would I set up my class and contrasts as: 5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa then use contrast [0.5 0.5 -0.33 -0.33

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

The first one will test for a difference between group offset/intercept accounting for age, gender, episodes, and residuals. By setting a regressor contrast element to 0, one accounts for that variable because the variable appears in the model that is fit to the data (and so its effects

[Freesurfer] mri_segment_hypothalamic_subunits 7.4.1 issue

External Email - Use Caution Dear FreeSurfer developers, I have just tested the Segmentation of hypothalamic subunits, but unfortunately it does not work. I simply wrote: mri_segment_hypothalamic_subunits --s subject_folder or mri_segment_hypothalamic_subunits --s