pyxnat · jhuguetn · May 14, 2025 · May 14, 2025 · May 14, 2025 · May 14, 2025
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 *.pyc
 MANIFEST
 pyxnat.egg-info/
+bbrc_pyxnat.egg-info/
 build/
 dist/
 *.DS_Store*

diff --git a/pyxnat/core/derivatives/donsurf.py b/pyxnat/core/derivatives/donsurf.py
@@ -1,8 +1,68 @@
 XNAT_RESOURCE_NAME = 'DONSURF'
 
 
-def aparc(self):
-    """Returns cortical features as estimated by `DONSURF`."""
+def aparc(self, metric='GM-MD'):
+    """
+    Retrieves cortical features as estimated by `DONSURF`.
 
-    from .freesurfer import aparc as fs_aparc
-    return fs_aparc(self)
+    Parameters
+    ----------
+    metric : str, optional
+        DONSURF metric to retrieve aparc statistics for. Available metrics
+        are 'GM-MD', 'GM-MD-koo', and 'SWM-MD'. Defaults to 'GM-MD'.
+
+    Returns
+    -------
+    pandas.DataFrame
+        Cortical DONSURF features for the selected `metric`.
+    """
+
+    import pandas as pd
+
+    volumes = ['BrainSegVol', 'BrainSegVolNotVent', 'BrainSegVolNotVentSurf',
+               'CortexVol', 'SupraTentorialVol', 'SupraTentorialVolNotVent',
+               'eTIV']
+    unitless = ['NumVert']
+    surfaces = ['WhiteSurfArea']
+    thickness = ['MeanThickness']
+    columns = ['StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg',
+               'ThickStd', 'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd']
+
+    table = []
+    if metric not in ['GM-MD', 'SWM-MD', 'GM-MD-koo']:
+        raise Exception(f'Invalid DONSURF metric "{metric}".')
+
+    files = list(self.files(f'{metric}/stats/*h.aparc.stats'))
+    for f in files:
+
+        uri = f._uri
+        side = {'l': 'left', 'r': 'right'}[uri.split('/')[-1][0]]
+
+        res = self._intf.get(uri).text.split('\n')
+
+        res2 = [e for e in res if e.startswith('# Measure ')]
+
+        measurements = {'Volume_mm3': volumes,
+                        'Thickness_mm': thickness,
+                        'SurfArea_mm2': surfaces,
+                        'unitless': unitless}
+
+        for unit, data in measurements.items():
+            for each in data:
+                m = [e for e in res2 if each == e.split(', ')[1]]
+                if len(m) == 1:
+                    m = float(m[0].split(', ')[-2])
+                    table.append([None, unit, each, m])
+
+        res2 = [e for e in res if not e.startswith('#')]
+        d2 = [[each for each in e.split(' ') if each != ''] for e in res2]
+        d2 = pd.DataFrame(d2, columns=columns).dropna()
+        d3 = d2.set_index('StructName').to_dict()
+
+        for m, aparc in d3.items():
+            for region, value in aparc.items():
+                row = [side, m, region, value]
+                table.append(row)
+
+    columns = ['side', 'measurement', 'region', 'value']
+    return pd.DataFrame(table, columns=columns)
diff --git a/pyxnat/core/derivatives/validator.py b/pyxnat/core/derivatives/validator.py
@@ -77,7 +77,7 @@ def extract_snapshots(fp):
         for page in range(len(doc)):
             xrefs.extend([img[0] for img in doc.get_page_images(page)])
         xrefs = sorted(set(xrefs))
-        for k, xref in enumerate(xrefs[1:]):
+        for k, xref in enumerate(xrefs):
             pix = fitz.Pixmap(doc, xref)
             fp_snap = op.join(dn, "{}_{}.png".format(bn, k))
             if pix.n >= 5:    # CMYK: convert to RGB first

diff --git a/pyxnat/tests/test_resource_functions.py b/pyxnat/tests/test_resource_functions.py
@@ -159,12 +159,15 @@ def test_cat12_volumes():
 
 def test_donsurf():
     r = e1.resource('DONSURF')
-    st = r.aparc()
-    left = float(st.query('measurement == "CurvInd" &'\
-                          'region == "insula" & side == "left"')['value'])
-    right = float(st.query('measurement == "CurvInd" &'\
-                           'region == "insula" & side == "right"')['value'])
-    assert(left == 15.7 and right == 15.8)
+    gm_md = r.aparc()
+    gm_md_pvc = r.aparc(metric='GM-MD-koo')
+    q = 'measurement == "ThickAvg" & region == "entorhinal" & side == "{side}"'
+    left = float(gm_md.query(q.format(side='left')).value.iloc[0])
+    right = float(gm_md.query(q.format(side='right')).value.iloc[0])
+    left_pvc = float(gm_md_pvc.query(q.format(side='left')).value.iloc[0])
+    right_pvc = float(gm_md_pvc.query(q.format(side='right')).value.iloc[0])
+    assert left == 7.25 and right == 7.534
+    assert left > left_pvc and right > right_pvc
 
 
 def test_freesurfer7_extras_brainstem_volumes():