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Dear AFNI users-

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Sincerely, AFNI HQ

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jreyelts
July 27, 2020 11:11PM
Hello,
I am trying to do a diffeomorphic warp for an analysis. We are trying to use the non-linear warp to more accurately map out an area of hypersignal. The script I used was to take an aligned T2 set (pic attached) and output a non-linear warp. What resulted is the second pic, which doesn't look quite right. What am I doing wrong? The script is as follows: 
if ( ! -f ${dset_pre}_WARP.nii.gz ) then
		echo "running nonlinear alignment with auto_warp for $subj"
		auto_warp.py -base $template -affine_input_xmat ID -qworkhard 0 2 \
		-input ${dset_pre}_aff${templateview} -overwrite \
		-output_dir awpy_${dset_pre} -qw_opts -iwarp
	
		cp awpy_${dset_pre}/anat.un.qw_WARP.nii ${dset_pre}_WARP.nii
		cp awpy_${dset_pre}/anat.un.qw_WARPINV.nii ${dset_pre}_WARPINV.nii
	
		gzip -f ${dset_pre}_WARP.nii ${dset_pre}_WARPINV.nii
	else
		echo "nonlinear alignment done for $subj"
	endif
	
	# combine nonlinear and affine warps for dataset warped to standard template space
	if ( ! -f ${dset_pre}_warp2std.nii.gz ) then
		echo "combining nonlinear and affine warps to warp original dataset to NMT space for $subj"
		3dNwarpApply -prefix ${dset_pre}_warp2std.nii.gz \
		-nwarp "${dset_pre}_WARP.nii.gz ${dset_pre}_al2std_mat.aff12.1D" \
		-source ${dset_pre}${dset_view} -master $template
	else
		echo "nonlinear and affine warps applied to original dataset for $subj"
	endif


Thank you for your help!



Edited 1 time(s). Last edit at 07/28/2020 09:02AM by ptaylor.
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Attachments:
open | download - aligned2std.PNG (275 KB)
open | download - warp2std.PNG (129 KB)
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Subject Author Posted

Help with diffeomorphic warping script Attachments

jreyelts July 27, 2020 11:11PM

Re: Help with diffeomorphic warping script

ptaylor July 28, 2020 09:10AM

Re: Help with diffeomorphic warping script

jreyelts July 28, 2020 01:39PM

Re: Help with diffeomorphic warping script

ptaylor July 28, 2020 02:46PM

Re: Help with diffeomorphic warping script

Daniel Glen July 29, 2020 05:37PM

Re: Help with diffeomorphic warping script

jreyelts July 29, 2020 11:33PM

Re: Help with diffeomorphic warping script

ptaylor July 30, 2020 09:29AM

Re: Help with diffeomorphic warping script

jreyelts August 08, 2020 07:33PM

Re: Help with diffeomorphic warping script

Daniel Glen August 09, 2020 08:48AM

Re: Help with diffeomorphic warping script

ptaylor August 10, 2020 02:54PM