Adds input data to registry

ME-ICA · Dec 6, 2022 · c7349bd · c7349bd
1 parent 9d22468
commit c7349bd
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Showing 5 changed files with 24 additions and 0 deletions.
diff --git a/tedana/resources/config/outputs.json b/tedana/resources/config/outputs.json
@@ -215,6 +215,10 @@
         "orig": "ica_orth_mixing",
         "bidsv1.5.0": "desc-ICAOrth_mixing"
     },
+    "input img": {
+        "orig": "raw_echo-{echo}",
+        "bidsv1.5.0": "echo-{echo}_desc-TedanaInput"
+    },
     "registry json": {
         "orig": "registry",
         "bidsv1.5.0": "desc-tedana_registry"

diff --git a/tedana/tests/data/cornell_three_echo_outputs.txt b/tedana/tests/data/cornell_three_echo_outputs.txt
@@ -24,6 +24,9 @@ desc-optcomAccepted_bold.nii.gz
 desc-optcomDenoised_bold.nii.gz
 desc-optcomRejected_bold.nii.gz
 desc-optcom_bold.nii.gz
+echo-1_desc-TedanaInput.nii.gz
+echo-2_desc-TedanaInput.nii.gz
+echo-3_desc-TedanaInput.nii.gz
 figures
 figures/carpet_optcom.svg
 figures/carpet_denoised.svg

diff --git a/tedana/tests/data/fiu_four_echo_outputs.txt b/tedana/tests/data/fiu_four_echo_outputs.txt
@@ -49,6 +49,7 @@ echo-1_desc-ICA_components.nii.gz
 echo-1_desc-PCAT2ModelPredictions_components.nii.gz
 echo-1_desc-PCAS0ModelPredictions_components.nii.gz
 echo-1_desc-PCA_components.nii.gz
+echo-1_desc-TedanaInput.nii.gz
 echo-1_desc-Rejected_bold.nii.gz
 echo-2_desc-Accepted_bold.nii.gz
 echo-2_desc-Denoised_bold.nii.gz
@@ -59,6 +60,7 @@ echo-2_desc-PCAT2ModelPredictions_components.nii.gz
 echo-2_desc-PCAS0ModelPredictions_components.nii.gz
 echo-2_desc-PCA_components.nii.gz
 echo-2_desc-Rejected_bold.nii.gz
+echo-2_desc-TedanaInput.nii.gz
 echo-3_desc-Accepted_bold.nii.gz
 echo-3_desc-Denoised_bold.nii.gz
 echo-3_desc-ICAT2ModelPredictions_components.nii.gz
@@ -68,6 +70,7 @@ echo-3_desc-PCAT2ModelPredictions_components.nii.gz
 echo-3_desc-PCAS0ModelPredictions_components.nii.gz
 echo-3_desc-PCA_components.nii.gz
 echo-3_desc-Rejected_bold.nii.gz
+echo-3_desc-TedanaInput.nii.gz
 echo-4_desc-Accepted_bold.nii.gz
 echo-4_desc-Denoised_bold.nii.gz
 echo-4_desc-ICAT2ModelPredictions_components.nii.gz
@@ -77,6 +80,7 @@ echo-4_desc-PCAT2ModelPredictions_components.nii.gz
 echo-4_desc-PCAS0ModelPredictions_components.nii.gz
 echo-4_desc-PCA_components.nii.gz
 echo-4_desc-Rejected_bold.nii.gz
+echo-4_desc-TedanaInput.nii.gz
 references.bib
 report.txt
 tedana_report.html

diff --git a/tedana/tests/data/nih_five_echo_outputs_verbose.txt b/tedana/tests/data/nih_five_echo_outputs_verbose.txt
@@ -42,6 +42,7 @@ echo-1_desc-PCAT2ModelPredictions_components.nii.gz
 echo-1_desc-PCAS0ModelPredictions_components.nii.gz
 echo-1_desc-PCA_components.nii.gz
 echo-1_desc-Rejected_bold.nii.gz
+echo-1_desc-TedanaInput.nii.gz
 echo-2_desc-Accepted_bold.nii.gz
 echo-2_desc-Denoised_bold.nii.gz
 echo-2_desc-ICAT2ModelPredictions_components.nii.gz
@@ -51,6 +52,7 @@ echo-2_desc-PCAT2ModelPredictions_components.nii.gz
 echo-2_desc-PCAS0ModelPredictions_components.nii.gz
 echo-2_desc-PCA_components.nii.gz
 echo-2_desc-Rejected_bold.nii.gz
+echo-2_desc-TedanaInput.nii.gz
 echo-3_desc-Accepted_bold.nii.gz
 echo-3_desc-Denoised_bold.nii.gz
 echo-3_desc-ICAT2ModelPredictions_components.nii.gz
@@ -60,6 +62,7 @@ echo-3_desc-PCAT2ModelPredictions_components.nii.gz
 echo-3_desc-PCAS0ModelPredictions_components.nii.gz
 echo-3_desc-PCA_components.nii.gz
 echo-3_desc-Rejected_bold.nii.gz
+echo-3_desc-TedanaInput.nii.gz
 echo-4_desc-Accepted_bold.nii.gz
 echo-4_desc-Denoised_bold.nii.gz
 echo-4_desc-ICAT2ModelPredictions_components.nii.gz
@@ -69,6 +72,7 @@ echo-4_desc-PCAT2ModelPredictions_components.nii.gz
 echo-4_desc-PCAS0ModelPredictions_components.nii.gz
 echo-4_desc-PCA_components.nii.gz
 echo-4_desc-Rejected_bold.nii.gz
+echo-4_desc-TedanaInput.nii.gz
 echo-5_desc-Accepted_bold.nii.gz
 echo-5_desc-Denoised_bold.nii.gz
 echo-5_desc-ICAT2ModelPredictions_components.nii.gz
@@ -78,6 +82,7 @@ echo-5_desc-PCAT2ModelPredictions_components.nii.gz
 echo-5_desc-PCAS0ModelPredictions_components.nii.gz
 echo-5_desc-PCA_components.nii.gz
 echo-5_desc-Rejected_bold.nii.gz
+echo-5_desc-TedanaInput.nii.gz
 references.bib
 report.txt
 tedana_report.html

diff --git a/tedana/workflows/tedana.py b/tedana/workflows/tedana.py
@@ -488,6 +488,14 @@ def tedana_workflow(
             "to correct your TR to the value it should be."
         )
 
+    # Save input data
+    for i in range(n_echos):
+        io_generator.save_file(
+            io.new_nii_like(ref_img, np.squeeze(catd[:, i, :])),
+            "input img",
+            echo=i + 1,
+        )
+
     if mixm is not None and op.isfile(mixm):
         mixm = op.abspath(mixm)
         # Allow users to re-run on same folder