[caret-users] ACPC Align Issue

[Donna Dierker]

Hi Traci,

Glad to hear you solved the index issue. As indicated off-list, these 
problems are hard to pin down.

John Harwell is on vacation for a week, and my knowledge of the inner 
workings of the AC-PC alignment routine is weak.

But I can see how it might need to pad in order to avoid cropping 
non-zero voxels from the original image. Imagine a volume that is 
already nearly AC-PC aligned, but the chin is rotated 5 degrees upward 
from the AC-PC line. To AC-PC align the image, the affine transform will 
need to produce a resulting image that, when viewed sagittally after 
transformation, will look like a slightly tilted rectangle. To avoid 
cropping the upper right and lower left corners, some slices will need 
to be added to either end. More abstractly, put one cracker on top of 
another cracker, so that their edges align perfectly. Now rotate the top 
cracker 45 degrees. It no longer fits in the bounding box defined by the 
lower cracker.

Donna

On 04/30/2009 05:17 PM, Sandoval, Traci I wrote:
>
> Hello All, I have found that when I acpc align my mprage file it is 
> changing the xyz dimensions, currently they are 160 x 256 x 256 after 
> acpc align, I save the file, then 3dinfo and my dimensions are 169 x 
> 262 x 256. the change is not consistent across brains, some become 
> 265, 296, 296 etc… It is causing a problem when I use the 
> –caret_command -volume combine - because the volume dimensions are 
> different. Thank you for all your help.
>
> PS. I resolved the bad-index issue, we had several paint files and it 
> was causing a problem, we have fixed it now. Thank you. Traci
>
> ___________________ _
>
> Traci Sandoval
> Research Assistant
> NeuroPsychometric Research Lab
> School of Behavioral and Brain Sciences - University of Texas at Dallas
> Center for BrainHealth - University of Texas at Dallas
> Department of Psychiatry - University of Texas Southwestern Medical Center
>
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