History of AFNI updates  

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March 12, 2019 12:14PM
Hi AFNI Experts,


I had a subject that I ran auto_warp.py once and the outputs had some line/vein artifacts. I took that output and ran auto_warp.py once more and the results came out great. When I concatenated the second set of transforms to apply to the original output of the first auto_warp.py things looked great. (3dNwarpApply -nwarp 'anat.rw.qw_WARP.nii anat.aff.Xat.1D' -source ../anat.aw.nii -prefix anat.final.nii. -interp wsinc5).

The problem comes when I want to concatenate all sets of warps together (3dNwarpApply -nwarp 'anat.rw.qw_WARP.nii anat.aff.Xat.1D ../anat.rw.qw_WARP.nii ../anat.aff.Xat.1D' -source ../anat.nii -prefix anat.final1.nii -interp wsinc5) I still get some line/vein artifact. I would like to combine all transforms so I can apply this warp to other data such as the T2 or BOLD imaging etc.


I also tried to run auto_warp.py (second time) and pass an -iniwarp of the original anat.rw.qw_WARP.nii anat.aff.Xat.1D and then a second time turning affine off so I just get a nonlinear warp and running with iniwarp and in all cases I still get the artifact. The only way this does not occur is if I warp the files once using the original transform and then warping that output again using the newer warp/affine parameters. Could it be a precision error when using a small patch size(minpatch 5) and combining warps? Does 3dNwarpApply use the affine matrix as part of the qform/sform in the same fashion as when writing the file out?

Is there a different way to implement combining warps when using multiple sets of transforms or better way to use iniwarp? I played around with adding IDENT(anat.aw.nii) and different combos of this with no success.

Any suggestions would be much appreciated.

Best,
Ajay
Subject Author Posted

Nonlinear transform EPI data

bunger October 30, 2018 01:55PM

Re: Nonlinear transform EPI data

Peter Molfese October 30, 2018 02:13PM

Re: Nonlinear transform EPI data

bunger October 30, 2018 04:51PM

Re: Nonlinear transform EPI data

rick reynolds October 30, 2018 05:00PM

Re: Nonlinear transform EPI data

mbrucks December 04, 2018 03:11PM

Re: Nonlinear transform EPI data

rick reynolds December 04, 2018 04:11PM

Re: Nonlinear transform EPI data

AjaySK March 12, 2019 12:14PM

Re: Nonlinear transform EPI data

Peter Molfese March 12, 2019 02:44PM

Re: Nonlinear transform EPI data

AjaySK March 12, 2019 04:02PM

Re: Nonlinear transform EPI data

RWCox March 13, 2019 11:24AM



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