[Freesurfer] Masking cortical thickness

2018-02-13 Thread James Hobart
Hi all, I am looking to mask out a small region of the GM when calculating the cortical thickness of ROIs across the brain. Essentially I have a couple of cases with small GM lesions where the cortical thickness is less likely to be meaningful for my analysis. I have binary lesion masks and also

[Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

2018-06-26 Thread James Hobart
External Email - Use Caution Hi Freesurfer community, I have an issue in adding a surface label to an annot file. I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf

Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

2018-07-23 Thread James Hobart
External Email - Use Caution Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended! Any help would be greatly appreciated. BW James On Tue, Jun 26, 2018 at 1:20 PM, James Hobart wrote: >