Traci wrote: > It is causing a problem when I use the –caret_command -volume combine > - because the volume dimensions are different. I didn't address this question.
And honestly I'm not sure how to do it using Caret's AC-PC alignment tool. (If John knows how, he can respond when he returns next week.) One can definitely write out the affine transform that Caret computes, and then you might be able to use AFNI's 3dWarp to apply it and write the resulting volume out in a specified grid (e.g., like volume A). But if you are combining volumes, you should also consider taking the AC-PC alignment a step further to affine registering your subjects to a common target, which would also get you the common grid that you need. You might not like the idea of normalizing for scale, but there is no doubt that it will improve alignment across subjects, resulting in a tighter/crisper mean/sum volume. On May 1, 2009, at 9:13 AM, Donna Dierker wrote: > >> 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 >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
