Refactored examples

pyushkevich · Dec 5, 2024 · ebf8b81 · ebf8b81
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diff --git a/.gitignore b/.gitignore
@@ -167,3 +167,4 @@ cython_debug/
 
 .*~
 .DS_Store
+sample_data/*/*/crashs
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/affine_t1_to_template/t1_to_template_affine.mat b/sample_data/ashs_pmc_alveus/subj02/ashs/affine_t1_to_template/t1_to_template_affine.mat
@@ -0,0 +1,4 @@
+0.957721 0.0381103 0.0271213 5.05427 
+-0.00325824 0.982826 -0.205419 -29.2906 
+-0.0230343 0.143985 1.00653 -14.9662 
+0 0 0 1 
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/final/subj02_left_lfseg_heur.nii.gz b/sample_data/ashs_pmc_alveus/subj02/ashs/final/subj02_left_lfseg_heur.nii.gz
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/final/subj02_right_lfseg_heur.nii.gz b/sample_data/ashs_pmc_alveus/subj02/ashs/final/subj02_right_lfseg_heur.nii.gz
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/flirt_t2_to_t1/flirt_t2_to_t1.mat b/sample_data/ashs_pmc_alveus/subj02/ashs/flirt_t2_to_t1/flirt_t2_to_t1.mat
@@ -0,0 +1,4 @@
+0.999962 -0.00839422 -0.0022024 -0.302938 
+0.00835345 0.999805 -0.0179078 -0.0370463 
+0.00235229 0.0178887 0.999837 -1.40911 
+0 0 0 1 
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat b/sample_data/ashs_pmc_alveus/subj02/ashs/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
@@ -0,0 +1,4 @@
+0.999963 0.00835346 0.00235229 0.306551
+-0.00839422 0.999804 0.0178887 0.0597033
+-0.0022024 -0.0179078 0.999837 1.40755
+0 0 0 1
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/mprage.nii.gz b/sample_data/ashs_pmc_alveus/subj02/ashs/mprage.nii.gz
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/tse_native_chunk_left.nii.gz b/sample_data/ashs_pmc_alveus/subj02/ashs/tse_native_chunk_left.nii.gz
diff --git a/sample_data/ashs_pmc_alveus/subj02/ashs/tse_native_chunk_right.nii.gz b/sample_data/ashs_pmc_alveus/subj02/ashs/tse_native_chunk_right.nii.gz
diff --git a/sample_data/ashs_pmc_alveus/subj02/readme.txt b/sample_data/ashs_pmc_alveus/subj02/readme.txt
@@ -0,0 +1 @@
+This folder contains ASHS output with ASHS PMC atlas for ADNI participant 003_S_4441 timepoint 2021-04-08.
diff --git a/..._t1_to_template/t1_to_template_affine.mat → ..._t1_to_template/t1_to_template_affine.mat b/..._t1_to_template/t1_to_template_affine.mat → ..._t1_to_template/t1_to_template_affine.mat
diff --git a/...n/posterior_corr_usegray_right_000.nii.gz → ...n/posterior_corr_usegray_right_000.nii.gz b/...n/posterior_corr_usegray_right_000.nii.gz → ...n/posterior_corr_usegray_right_000.nii.gz
diff --git a/...n/posterior_corr_usegray_right_001.nii.gz → ...n/posterior_corr_usegray_right_001.nii.gz b/...n/posterior_corr_usegray_right_001.nii.gz → ...n/posterior_corr_usegray_right_001.nii.gz
diff --git a/...n/posterior_corr_usegray_right_002.nii.gz → ...n/posterior_corr_usegray_right_002.nii.gz b/...n/posterior_corr_usegray_right_002.nii.gz → ...n/posterior_corr_usegray_right_002.nii.gz
diff --git a/...n/posterior_corr_usegray_right_007.nii.gz → ...n/posterior_corr_usegray_right_007.nii.gz b/...n/posterior_corr_usegray_right_007.nii.gz → ...n/posterior_corr_usegray_right_007.nii.gz
diff --git a/...n/posterior_corr_usegray_right_009.nii.gz → ...n/posterior_corr_usegray_right_009.nii.gz b/...n/posterior_corr_usegray_right_009.nii.gz → ...n/posterior_corr_usegray_right_009.nii.gz
diff --git a/...n/posterior_corr_usegray_right_010.nii.gz → ...n/posterior_corr_usegray_right_010.nii.gz b/...n/posterior_corr_usegray_right_010.nii.gz → ...n/posterior_corr_usegray_right_010.nii.gz
diff --git a/...n/posterior_corr_usegray_right_011.nii.gz → ...n/posterior_corr_usegray_right_011.nii.gz b/...n/posterior_corr_usegray_right_011.nii.gz → ...n/posterior_corr_usegray_right_011.nii.gz
diff --git a/...n/posterior_corr_usegray_right_012.nii.gz → ...n/posterior_corr_usegray_right_012.nii.gz b/...n/posterior_corr_usegray_right_012.nii.gz → ...n/posterior_corr_usegray_right_012.nii.gz
diff --git a/...n/posterior_corr_usegray_right_013.nii.gz → ...n/posterior_corr_usegray_right_013.nii.gz b/...n/posterior_corr_usegray_right_013.nii.gz → ...n/posterior_corr_usegray_right_013.nii.gz
diff --git a/...n/posterior_corr_usegray_right_014.nii.gz → ...n/posterior_corr_usegray_right_014.nii.gz b/...n/posterior_corr_usegray_right_014.nii.gz → ...n/posterior_corr_usegray_right_014.nii.gz
diff --git a/...n/posterior_corr_usegray_right_016.nii.gz → ...n/posterior_corr_usegray_right_016.nii.gz b/...n/posterior_corr_usegray_right_016.nii.gz → ...n/posterior_corr_usegray_right_016.nii.gz
diff --git a/...n/posterior_corr_usegray_right_017.nii.gz → ...n/posterior_corr_usegray_right_017.nii.gz b/...n/posterior_corr_usegray_right_017.nii.gz → ...n/posterior_corr_usegray_right_017.nii.gz
diff --git a/...n/posterior_corr_usegray_right_020.nii.gz → ...n/posterior_corr_usegray_right_020.nii.gz b/...n/posterior_corr_usegray_right_020.nii.gz → ...n/posterior_corr_usegray_right_020.nii.gz
diff --git a/sample_data/ashs_pmc_t1/subj01/readme.txt b/sample_data/ashs_pmc_t1/subj01/readme.txt
@@ -0,0 +1 @@
+This folder contains partial ASHS output with 2023 ASHS-T1 PMC atlas for ADNI participant 035_S_4082 timepoint 2011-06-28
Original file line number	Diff line number	Diff line change
Expand Up		@@ -167,3 +167,4 @@ cython_debug/

		.*~
		.DS_Store
		sample_data///crashs
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This folder contains ASHS output with ASHS PMC atlas for ADNI participant 003_S_4441 timepoint 2021-04-08.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This folder contains partial ASHS output with 2023 ASHS-T1 PMC atlas for ADNI participant 035_S_4082 timepoint 2011-06-28