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October 30, 2018 02:13PM
You should use auto_warp.py to normalize your T1 to MNI space. And then use 3dNwarpApply to apply that transform to your EPI data.

There is a new tool: @SSwarper that will take care of the skull stripping and nonlinear warping (via 3dQwarp) your T1 to MNI space, and then you can use 3dNwarpApply to apply the transformation to your EPI dataset. You'll see in the help, there are also hooks in afni_proc.py for taking the output of @SSwarper and doing all the other processing on your EPI datasets.

-Peter
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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