Add a node for selecting specific shells from preprocessed dwis (#194)

--------- Co-authored-by: Taylor Salo <[email protected]>
PennLINC · Dec 6, 2024 · f95211a · f95211a
1 parent 9bd2036
commit f95211a
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Showing 15 changed files with 454 additions and 36 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -249,6 +249,25 @@ jobs:
       - store_artifacts:
           path: /src/qsirecon/.circleci/out/multises_post1_qsiprep_reportsession/
 
+  Recon_Interfaces:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: multishell_output-01
+      - run: *runinstall
+      - run:
+          name: Pytest the recon interfaces
+          no_output_timeout: 1h
+          command: |
+            pytest -rP -o log_cli=true -m "interfaces" --cov-config=/src/qsirecon/pyproject.toml --cov-append --cov-report term-missing --cov=qsirecon --data_dir=/src/qsirecon/.circleci/data --output_dir=/src/qsirecon/.circleci/out --working_dir=/src/qsirecon/.circleci/work qsirecon
+            mkdir /src/coverage
+            mv /src/qsirecon/.coverage /src/coverage/.coverage.recon_interfaces
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.recon_interfaces
+
   Recon_MRtrix3:
     <<: *dockersetup
     steps:
@@ -632,6 +651,13 @@ workflows:
             tags:
               only: /.*/
 
+      - Recon_Interfaces:
+          requires:
+            - download_multishell_output
+          filters:
+            tags:
+              only: /.*/
+
       - Recon_AutoTrack:
           requires:
             - download_multishell_output
@@ -693,6 +719,7 @@ workflows:
             - Recon_3Tissue_Singleshell_ACT
             - Recon_3Tissue_Singleshell_NoACT
             - Recon_MRtrix3
+            - Recon_Interfaces
             - Recon_AutoTrack
             - Recon_Tortoise
             - Recon_DIPY_MAPMRI
@@ -717,6 +744,7 @@ workflows:
             - Recon_3Tissue_Singleshell_ACT
             - Recon_3Tissue_Singleshell_NoACT
             - Recon_MRtrix3
+            - Recon_Interfaces
             - Recon_msmt_Multishell_HSVS
             - Recon_AutoTrack
             - Recon_Tortoise

diff --git a/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_ACT-fast.yaml b/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_ACT-fast.yaml
@@ -2,8 +2,18 @@ anatomical:
 - mrtrix_5tt_fast
 name: mrtrix_singleshell_ss3t_fast
 nodes:
--   action: csd
+
+-   action: select_gradients
     input: qsirecon
+    name: select_single_shell
+    parameters:
+        requested_shells:
+            - 0
+            - highest
+        bval_distance_cutoff: 100
+
+-   action: csd
+    input: select_single_shell
     name: ss3t_csd
     parameters:
         fod:

diff --git a/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_ACT-hsvs.yaml b/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_ACT-hsvs.yaml
@@ -2,8 +2,16 @@ anatomical:
 - mrtrix_5tt_hsvs
 name: mrtrix_singleshell_ss3_hsvst
 nodes:
--   action: csd
+-   action: select_gradients
     input: qsirecon
+    name: select_single_shell
+    parameters:
+        requested_shells:
+            - 0
+            - highest
+        bval_distance_cutoff: 100
+-   action: csd
+    input: select_single_shell
     name: ss3t_csd
     parameters:
         fod:

diff --git a/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_noACT.yaml b/qsirecon/data/pipelines/mrtrix_singleshell_ss3t_noACT.yaml
@@ -1,8 +1,18 @@
 anatomical: []
 name: mrtrix_singleshell_ss3t_noACT
 nodes:
--   action: csd
+
+-   action: select_gradients
     input: qsirecon
+    name: select_single_shell
+    parameters:
+        requested_shells:
+            - 0
+            - highest
+        bval_distance_cutoff: 100
+
+-   action: csd
+    input: select_single_shell
     name: ss3t_csd
     parameters:
         fod:

diff --git a/qsirecon/data/schemes/DSIQ5.bval b/qsirecon/data/schemes/DSIQ5.bval
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diff --git a/qsirecon/data/schemes/DSIQ5.bvec b/qsirecon/data/schemes/DSIQ5.bvec
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