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 N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

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 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 some sort of inverse mni152.register.dat somewhere?

Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu> wrote:

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

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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 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 threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer