[Freesurfer] Cerebellar Parcellation Viewing and Corrections

Hi all, I apologize if it is well documented and I am just not seeing it but is there a way to view and edit cerebellar parcellations? Thanks, Alex Rockhill Translational Neuroengineering Laboratory Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charle

Re: [Freesurfer] -qcache in recon-all commnd

External Email - Use Caution Any further comments on the correct command to run after making manual edits. Specifically, should the '-hippocampal-subfields-T1' flag be used again in the rerun 'recon-all -all' command after manual edits? Jim "The materials in this email are priv

Re: [Freesurfer] Lookup table to surface overlay

You might be sampling outside of the brain. Try adding --projabs -2 To sample 2mm below the pial surface On 5/25/18 10:32 AM, Funk, Quentin wrote: Freesurfer experts, I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Cu

[Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity

Hello, I'm interested in looking into the association of cortical thickness and white matter hyperintensity from a regional perspective. Specifically, I would like to create a figure that depicts in which ROIs does cortical thinning correlate significantly with increased white matter hyperinte

Re: [Freesurfer] RAS coordinates for inflated surface

no worries, I'm glad it worked out Bruce On Fri, 25 May 2018, Giulia Liberati wrote: External Email - Use Caution Hi Bruce, You are right. There was a silly bug in my plotting script which I managed to fix. So now everything is at its place! Thank you very much for your pa

Re: [Freesurfer] RAS coordinates for inflated surface

External Email - Use Caution Hi Bruce, You are right. There was a silly bug in my plotting script which I managed to fix. So now everything is at its place! Thank you very much for your patience and support! Giulia 2018-05-25 15:52 GMT+02:00 Bruce Fischl : > Hi Giulia, > > n

[Freesurfer] Lookup table to surface overlay

External Email - Use Caution Freesurfer experts, I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Currently I'm using this command: mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp nearest

Re: [Freesurfer] fthresh function in tksurfer

I don't know anything about neuroelf, but unless your have a binarized map, then the map is going to change when you change the threshold. BTW, if you wan to use freeview, you can run tksurferfv with the same args as tksurfer On 5/22/18 3:49 PM, srishti goel wrote: Hello, I am trying to v

Re: [Freesurfer] RAS coordinates for inflated surface

Hi Giulia, no, that shouldn't be the case. You don't care about the RAS coordinates of the inflated vertex - only its index. Use the index to look up the corresponding vertex on another surface like white, then use its RAS coords. Should work for any spot in the brain. cheers Bruce On Fri, 2

Re: [Freesurfer] RAS coordinates for inflated surface

External Email - Use Caution I will try to to show you an example of the issue, so it may be clearer. Let's say I have a contact in the left posterior insula with MNI coordinates -33, -12, 13. This corresponds to vertex 4983. RAS coordinates on a pial surface: -35.1280 -10.8052