Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:00 PM, Douglas

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

I don't understand what you mean by a much smaller brain. Can you elaborate? On 10/01/2013 06:10 PM, Yang, Daniel wrote: Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel --

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

I thinkyou just need to change the aparc to be either transparent or outline. On 10/01/2013 07:44 PM, Yang, Daniel wrote: Hi Doug, I think I find out where the problem is. Actually the mri_vol2surf works nicely (and it's also true that tksurfer with -mni152reg samples the overlay to the

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the

[Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same