84 lines
2.6 KiB
Bash
84 lines
2.6 KiB
Bash
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#!/usr/bin/env bash
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. "$(dirname "$0")/../test.sh"
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t() { test_command mri_synthmorph "$@" ; }
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# affine registration
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t -m affine -o out.mgz moving.mgz fixed.mgz
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compare_vol out.mgz affine.mgz --thresh 0.02
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# affine symmetry
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t -m aff -O out.mgz fixed.mgz moving.mgz
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compare_vol out.mgz affine.mgz --thresh 0.02
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# affine inverse consistency
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t -m a -t out.lta -T inv.lta moving.mgz fixed.mgz
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lta_diff out.lta inv.lta --invert2 | awk 'END {print $0; exit !($0<1e-3)}'
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# output directory creation
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t -ma -d outputs fixed.mgz moving.mgz
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[ -d outputs ]
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# rigid inverse consistency
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t -m rigid -t out.lta -T inv.lta moving.mgz fixed.mgz
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lta_diff out.lta inv.lta --invert2 | awk 'END {print $0; exit !($0<1e-3)}'
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# rigid registration
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t -m rig -o out.mgz moving.mgz fixed.mgz
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compare_vol out.mgz rigid.mgz --thresh 0.02
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# geometry update
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t -m r -Ho out.mgz moving.mgz fixed.mgz
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compare_vol out.mgz header.mgz --thresh 0.02 --res-thresh 1e-3 --geo-thresh 1e-3
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# deformable registration with initialization
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t -m deform -i affine.lta -o out_1.mgz -O out_2.mgz moving.mgz fixed.mgz
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compare_vol out_1.mgz deform_1.mgz --thresh 0.02
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compare_vol out_2.mgz deform_2.mgz --thresh 0.02
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# deformable registration with mid-space initialization
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t -m def -Mi affine.lta -o out.nii.gz moving.mgz fixed.mgz
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compare_vol out.nii.gz deform_mid.nii.gz --thresh 0.02 --geo-thresh 1e-4
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# joint registration
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t -m joint -o out.mgz moving.mgz fixed.mgz
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compare_vol out.mgz joint.mgz --thresh 0.02
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# default model
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t -o out.mgz moving.mgz fixed.mgz
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compare_vol out.mgz joint.mgz --thresh 0.02
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# help, usage, command abbreviation
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FSTEST_NO_DATA_RESET=1
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t register -h
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for cmd in r re reg regi regis registe register; do
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t "$cmd"
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done
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# deformable flags, explicit command
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t register moving.mgz fixed.mgz -md -j16 -e256 -n7 -r0.5
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t register moving.mgz fixed.mgz -m j -j 16 -e 192 -n 5 -r 0.7
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# NIfTI warps
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FSTEST_NO_DATA_RESET=1
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mri_convert=$(find_path $FSTEST_CWD mri_convert/mri_convert)
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t -t out.nii.gz moving.mgz fixed.mgz
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test_command $mri_convert -odt float -at out.nii.gz moving.mgz out.mgz
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compare_vol out.mgz joint.mgz --thresh 1
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# displacements in RAS space
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mri_warp_convert=$(find_path $FSTEST_CWD mri_warp_convert/mri_warp_convert)
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test_command $mri_warp_convert -g moving.mgz --inras out.nii.gz --outmgzwarp out.mgz
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test_command $mri_convert -odt float -at out.mgz moving.mgz moved.mgz
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compare_vol moved.mgz joint.mgz --thresh 1 --geo-thresh 1e-4
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# illegal arguments
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EXPECT_FAILURE=1
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t moving.mgz fixed.mgz -m banana
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t moving.mgz fixed.mgz -e 1
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t moving.mgz fixed.mgz -n 4
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t moving.mgz fixed.mgz -r 0
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t moving.mgz fixed.mgz -r 1
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t moving.mgz fixed.mgz -Hm deform
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t moving.mgz fixed.mgz -Hm joint
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