added eddy qc to report

GalKepler · Aug 5, 2024 · 972a5f2 · 972a5f2
1 parent a0d7f4f
commit 972a5f2
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Showing 4 changed files with 6 additions and 200 deletions.
diff --git a/src/keprep/data/quality_assurance/templates/reports-spec copy.yml b/src/keprep/data/quality_assurance/templates/reports-spec copy.yml
diff --git a/src/keprep/data/quality_assurance/templates/reports-spec.yml b/src/keprep/data/quality_assurance/templates/reports-spec.yml
@@ -42,6 +42,9 @@ sections:
     caption: b=0 to anatomical reference registration
     subtitle: Coregistration of the DWI to the anatomical T1w image using FSL's <code>FLIRT</code>.
     static: false
+  - bids: {datatype: figures, desc: eddyqc, suffix: dwi}
+    caption: EDDY Quality Control
+    subtitle: QC for head motion correction as conducted by FSL's <code>EDDY</code>.
 
 
 - name: About

diff --git a/src/keprep/workflows/dwi/stages/post_eddy.py b/src/keprep/workflows/dwi/stages/post_eddy.py
@@ -59,7 +59,7 @@ def init_post_eddy_wf(name: str = "post_eddy_wf") -> pe.Workflow:
         ),
         name="plot_eddy_qc",
     )
-    plot_eddy_qc_node.inputs.out_file = "eddy_qc_plot.png"
+    plot_eddy_qc_node.inputs.out_file = "eddy_qc_plot.svg"
     workflow.connect(
         [
             (

diff --git a/src/keprep/workflows/dwi/utils.py b/src/keprep/workflows/dwi/utils.py
@@ -53,6 +53,7 @@ def plot_eddy_qc(
     dpi : int, optional
         dpi of the plot (default: 300)
     """
+    import os
     from pathlib import Path
 
     import matplotlib.pyplot as plt
@@ -149,6 +150,7 @@ def plot_eddy_qc(
     plt.tight_layout()
 
     # save the plot with transparent background
+    out_file = os.getcwd() + "/" + out_file
     plt.savefig(out_file, dpi=dpi, bbox_inches="tight", transparent=True)
     plt.close()