Thanks, Doug!

I made that rectangle mark on the forehead actually.

According to your suggestion, I tried tkmedit test orig.mgz -overlay test_mark.img -overlay-reg reg.dat The only mark that I could find is on the left side of the image in coronal view and nothing in sagittal view. So there is something wrong.

Then I tried thregister2 --targ ./test/mri/orig/001.mgz --mov test_mark.img –reg reg.dat The mark is still in the forehead with sagittal view. I compared all three views (coronal, sagittal and horizontal) between target and moveable. It seemed they were coregisterd very well.

When I overlaid test_mark.img on the brain surface, the mark is located in the bottom of the brain.

Do I explain all these clearly?

Thanks for the help! Elva

Quoting Doug Greve greve@nmr.mgh.harvard.edu:

In step 3, was the registration correct?

You can also try:

tkmedit test orig.mgz -overlay test_mark.img -overlay-reg reg.dat

the mark should be in the right place.

qz4@ee.duke.edu wrote:

...

Hi all,

I got some problems when I tried to overlay some maps one brain surface. The

...

following steps is just for test.

1.    recon-all -all -notalairach -i MP-rage/001.dcm –s test
   

2.    I use matlab to load the save dataset (MP-rage/001.dcm ~ 160.dcm)
   

...

and then mark the back-head (>1000). The output is test_mark.img (analyze

format)

...

3.    thregister2 --targ ./test/mri/orig/001.mgz --mov test_mark.img –
   

regheader –reg reg.dat So I got reg.dat in this step 4. thsurfer test lh inflated --overlay test_mark.img –overlay-reg reg.dat –fthresh 1000 The weird thing happened in the final surface image. The mark is not shown

in

...

back-head. It is located in the botton of the brain surface. If in the 4, I do the following instead (no registration) thsurfer test lh inflated --overlay test_mark.img --fthresh 1000 The mark is in the right location (back-head), but a little offset.

What’s wrong in my procedure? Am I doing right in the registion part? Is it

...

correct to register to /mri/orig/001.mgz?

Thanks! Elva

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