Great! I see what you mean .. I think I just see some residual overlay in the medial wall when I load aparc.annot…
Thanks so much! -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 10/1/13 7:53 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
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 white surface by default instead of to the pial surface.)
The problem is in freeview + rh.aparc.annot.
If you do the following for the attached rh mgh file, you will see it correctly displayed:
tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh
If you overlay this mgh in freeview with rh.inflated surface, but without loading rh.aparc.annot, it also displays correctly.
However, once I load the rh.aparc.annot, I see something like attached png.
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 10/1/13 6:11 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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
-- 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 mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu%3E> 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 mailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu%3E mailto:yung-jui.yang@yale.edu%3E%3E> 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 mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu%3E mailto:greve@nmr.mgh.harvard.edu%3E%3E> 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
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-- 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/
-- 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/