Re: [Freesurfer] Thalamus segmentation

Yes! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of sara ponticorvo Reply-To: Freesurfer support list Date: Tuesday, 14 January 2020 at 17:45 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Thalamus

[Freesurfer] Extract specific LGI and Volume values

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my lo

Re: [Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics

External Email - Use Caution Thank you very much! Much appreciated Prof Leo. On Tue, Jan 14, 2020, 6:46 PM Thomas Yeo wrote: > Hi Kate, > > You can see the instructions here: > https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_Loca

[Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics

External Email - Use Caution Dear Freesurfer team, I would like to include Schaefer atlas into freesurfer. The Schaefer atlas can be found in the link below: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations

Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces

if the gray matter you are interested looks ok then you should be fine Bruce On Tue, 14 Jan 2020, Rachel Hoel wrote: External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at

[Freesurfer] Thalamus segmentation

External Email - Use Caution Hi Freesurfer expert, I have a question regarding the segmentation of the thalamus. After the “standard” segmentation from the recon-all (aseg), in label thalamus-Proper is included the medial geniculate body? Thanks, Sara _

Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces

External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at grey matter data, do we need to be concerned if the subcortical segmentation isn’t accurate? Best, Rachel __

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

External Email - Use Caution Hello, I was wondering if someone could answer my question below Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files. Are there any set of parameters that should be set differently when using pc1 instead of thickness files? Tha