Add tests and test data for 5ttgen msmt

MRtrix3 · Oct 22, 2024 · dddce99 · dddce99
1 parent 53a5ac5
commit dddce99
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Showing 4 changed files with 44 additions and 2 deletions.
diff --git a/testing/CMakeLists.txt b/testing/CMakeLists.txt
@@ -27,7 +27,7 @@ ExternalProject_Add(BinariesTestData
 ExternalProject_Add(ScriptsTestData
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/scripts_data
     GIT_REPOSITORY ${mrtrix_scripts_data_url}
-    GIT_TAG 76f47633cd0a37e901c42320f4540ecaffd51367
+    GIT_TAG ed1d3c630db9eafd6ce2808360e9e99529abfabc
     GIT_PROGRESS TRUE
     CONFIGURE_COMMAND ""
     BUILD_COMMAND ""
@@ -47,4 +47,4 @@ add_subdirectory(binaries)
 add_subdirectory(lib)
 add_subdirectory(scripts)
 add_subdirectory(tools)
-add_subdirectory(unit_tests)
+add_subdirectory(unit_tests)
diff --git a/testing/scripts/CMakeLists.txt b/testing/scripts/CMakeLists.txt
@@ -47,6 +47,8 @@ add_bash_script_test(5ttgen/hsvs_piping)
 add_bash_script_test(5ttgen/hsvs_template)
 add_bash_script_test(5ttgen/hsvs_whitespace)
 add_bash_script_test(5ttgen/hsvs_whitestem)
+add_bash_script_test(5ttgen/msmt_default)
+add_bash_script_test(5ttgen/msmt_masked)
 
 add_bash_script_test(dwi2mask/3dautomask_default)
 add_bash_script_test(dwi2mask/3dautomask_options)

diff --git a/testing/scripts/tests/5ttgen/msmt_default b/testing/scripts/tests/5ttgen/msmt_default
@@ -0,0 +1,19 @@
+#!/bin/bash
+# Verify "5ttgen msmt" default operation
+# Output is compared to a prior output generateed by the command
+
+# First we need to get some multi-tissue ODFs
+dwi2response dhollander BIDS/sub-01/dwi/sub-01_dwi.nii.gz tmp_wm.txt tmp_gm.txt tmp_csf.txt \
+-fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval \
+-mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz \
+-force
+dwi2fod msmt_csd BIDS/sub-01/dwi/sub-01_dwi.nii.gz \
+-fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval \
+tmp_wm.txt tmp_wm.mif \
+tmp_gm.txt tmp_gm.mif \
+tmp_csf.txt tmp_csf.mif \
+-force
+
+5ttgen msmt tmp_wm.mif tmp_gm.mif tmp_csf.mif tmp.mif -force
+
+testing_diff_image tmp.mif 5ttgen/msmt/default.mif.gz -abs 1e-5
diff --git a/testing/scripts/tests/5ttgen/msmt_masked b/testing/scripts/tests/5ttgen/msmt_masked
@@ -0,0 +1,21 @@
+#!/bin/bash
+# Verify "5ttgen msmt" operation where a user-specified mask is provided
+# Output is compared to a prior output generateed by the command
+
+# First we need to get some multi-tissue ODFs
+dwi2response dhollander BIDS/sub-01/dwi/sub-01_dwi.nii.gz tmp_wm.txt tmp_gm.txt tmp_csf.txt \
+-fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval \
+-mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz \
+-force
+dwi2fod msmt_csd BIDS/sub-01/dwi/sub-01_dwi.nii.gz \
+-fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval \
+tmp_wm.txt tmp_wm.mif \
+tmp_gm.txt tmp_gm.mif \
+tmp_csf.txt tmp_csf.mif \
+-force
+
+5ttgen msmt tmp_wm.mif tmp_gm.mif tmp_csf.mif tmp.mif \
+-mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz \
+-force
+
+testing_diff_image tmp.mif 5ttgen/msmt/masked.mif.gz -abs 1e-5