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Forum TrackVis Usage how to coregister the brain

how to coregister the brain
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UserPost

3:34 am
November 11, 2011


wl1971

Member

posts 4
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1

thank you for the answer  for my question  of how to draw the same ROI in two brain.

The answer of you

"You can save the ROI as a volume file and load it back in the other one, assuming both brains have the same geometry information. If not, you will need to coregister it first."

but how to do it? with trackvis or other software

11:33 am
November 14, 2011


Ruopeng

Admin

posts 406
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2

TrackVis can not do any coregistration. You'll need other software to do it, such FSL or Freesurfer.

Ruopeng

3:12 am
February 15, 2012


gaolion

Member

posts 17
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3

It's easy to co-register img files with FSL or SPM, but we can never co-register trackVIS files, as it needs to generate fibers.

Is that a correct statement on trackvis ?

Thank for the answer in advance!

Gao

5:12 pm
February 15, 2012


Ruopeng

Admin

posts 406
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4

Once you co-register img files, you will have a registration matrix file. You can apply that to track file in Diffusion Toolkit via "Track transform…".

Ruopeng

12:39 pm
February 17, 2012


gaolion

Member

posts 17
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5
Thanks for the suggestions.
I am using SPM, which seems failed to generate a suitable matrix file (pls see followed). I may try FSL/FreeSurf in the future. If you can also make a video or a figure on this, that would be very helpful.
Thank you very much!
Gao
..
Running 'Coregister: Estimate & Reslice'
iteration 1…
-1.517   0        0        0        0        0        | -1.0395
-1.517   -18.13   0        0        0        0        | -1.0491
-1.517   -18.13   14.07    0        0        0        | -1.0557
-1.517   -18.13   14.07    0.2499   0        0        | -1.0576
-1.517   -18.13   14.07    0.2499   0.01313  0        | -1.0577
-1.517   -18.13   14.07    0.2499   0.01313  0.08951  | -1.0584
iteration 2…
-0.367   -18.13   14.07    0.2499   0.01313  0.08951  | -1.0584
-0.367   -16.5    14.07    0.2499   0.01313  0.08951  | -1.0587
-0.367   -16.5    14.86    0.2499   0.01313  0.08951  | -1.0588
-0.367   -16.5    14.86    0.2426   0.01313  0.08951  | -1.0588
-0.367   -16.5    14.86    0.2426   -0.03467 0.08951  | -1.0589
-0.367   -16.5    14.86    0.2426   -0.03467 0.09089  | -1.0589
iteration 3…
-0.3021  -16.5    14.86    0.2426   -0.03467 0.09089  | -1.0589
-0.3021  -17.1    14.86    0.2426   -0.03467 0.09089  | -1.059
-0.3021  -17.1    14.92    0.2426   -0.03467 0.09089  | -1.059
-0.3021  -17.1    14.92    0.2426   -0.03467 0.09089  | -1.059
-0.3021  -17.1    14.92    0.2426   -0.03007 0.09089  | -1.059
-0.3021  -17.1    14.92    0.2426   -0.03007 0.09557  | -1.059
iteration 4…
-0.2254  -17.1    14.92    0.2426   -0.03007 0.09557  | -1.059
-0.2254  -17.27   14.92    0.2426   -0.03007 0.09557  | -1.059
-0.2254  -17.27   14.92    0.2426   -0.03007 0.09557  | -1.059
-0.2254  -17.27   14.92    0.2426   -0.03007 0.09557  | -1.059
-0.2254  -17.27   14.92    0.2426   -0.03007 0.09557  | -1.059
-0.2254  -17.27   14.92    0.2426   -0.03007 0.09544  | -1.059
iteration 5…
-0.1314  -17.27   14.92    0.2426   -0.03007 0.09544  | -1.059
-0.1314  -17.3    14.92    0.2426   -0.03007 0.09544  | -1.059
-0.1314  -17.3    14.92    0.2426   -0.03007 0.09544  | -1.059
-0.1314  -17.3    14.92    0.2426   -0.03007 0.09544  | -1.059
-0.1314  -17.3    14.92    0.2426   -0.03007 0.09544  | -1.059
-0.1314  -17.3    14.92    0.2426   -0.03007 0.09551  | -1.059
iteration 6…
-0.1251  -17.3    14.92    0.2426   -0.03007 0.09551  | -1.059
-0.1251  -17.3    14.92    0.2426   -0.03007 0.09551  | -1.059
-0.1251  -17.3    14.94    0.2426   -0.03007 0.09551  | -1.059
-0.1251  -17.3    14.94    0.2426   -0.03007 0.09551  | -1.059
-0.1251  -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.1251  -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
iteration 7…
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
iteration 8…
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
-0.09387 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.059
iteration 1…
-0.006601 -17.3    14.94    0.2426   -0.02863 0.09551  | -1.0586
-0.006601 -17.13   14.94    0.2426   -0.02863 0.09551  | -1.0586
-0.006601 -17.13   14.94    0.2426   -0.02863 0.09551  | -1.0586
-0.006601 -17.13   14.94    0.2499   -0.02863 0.09551  | -1.0586
-0.006601 -17.13   14.94    0.2499   -0.01791 0.09551  | -1.0586
-0.006601 -17.13   14.94    0.2499   -0.01791 0.08001  | -1.0586
iteration 2…
-0.006601 -17.13   14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.006601 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.006601 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.006601 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.006601 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.006601 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
iteration 3…
-0.002834 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.002834 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.002834 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.002834 -17      14.94    0.2499   -0.01791 0.08001  | -1.0586
-0.002834 -17      14.94    0.2499   -0.01778 0.08001  | -1.0586
-0.002834 -17      14.94    0.2499   -0.01778 0.08001  | -1.0586

12:10 pm
February 22, 2012


Ruopeng

Admin

posts 406
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6

Sorry I'm not familar with SPM. But in any case, when co-registration is done, there should be a definitive transformation matrix calculated from source to target.

Ruopeng
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