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[CI]: Fix examples #352

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merged 5 commits into from
Jul 19, 2024
Merged

[CI]: Fix examples #352

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bb91926
Fix example
fraimondo Jul 18, 2024
2a1c432
Fix main CI
fraimondo Jul 18, 2024
8587e2f
Fix RSSETS example
fraimondo Jul 18, 2024
6c621b8
typo
fraimondo Jul 18, 2024
739b09b
chore: fix examples/run_junifer_julearn.py
synchon Jul 19, 2024
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4 changes: 2 additions & 2 deletions examples/run_compute_parcel_mean.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
feature = marker.fit_transform(element_data)
# Print the output
print(feature.keys())
print(feature["VBM_GM"]["data"].shape) # Shape is (1 x parcels)
print(feature["VBM_GM"]["aggregation"]["data"].shape) # Shape is (1 x parcels)

###############################################################################
# Perform parcel aggregation on BOLD data (4D) from SPM Auditory dataset
Expand All @@ -54,4 +54,4 @@
feature = marker.fit_transform(element_data)
# Print the output
print(feature.keys())
print(feature["BOLD"]["data"].shape) # Shape is (timepoints x parcels)
print(feature["BOLD"]["aggregation"]["data"].shape) # Shape is (timepoints x parcels)
4 changes: 2 additions & 2 deletions examples/run_ets_rss_marker.py
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Expand Up @@ -70,8 +70,8 @@
# List all the features
print(db.list_features())
# Read extracted features
df_vbm = db.read_df(feature_name="BOLD_Schaefer100x17_RSSETS")
df_rssets = db.read_df(feature_name="BOLD_Schaefer200x17_RSSETS_rss_ets")

###############################################################################
# Now we take a look at the dataframe
df_vbm.head()
df_rssets.head()
2 changes: 1 addition & 1 deletion examples/run_junifer_julearn.py
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Expand Up @@ -84,7 +84,7 @@
collect(storage)
db = SQLiteFeatureStorage(uri=storage["uri"])

df_vbm = db.read_df(feature_name="VBM_GM_Schaefer200x17_Mean")
df_vbm = db.read_df(feature_name="VBM_GM_Schaefer200x17_Mean_aggregation")
oasis_subjects = [x[0] for x in df_vbm.index]
df_vbm.index = oasis_subjects

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8 changes: 6 additions & 2 deletions junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py
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Expand Up @@ -136,8 +136,12 @@ def compute(
method=self.correlation_method,
).values,
# Columns should be named after parcellation 1
"col_names": aggregation_parcellation_one["col_names"],
"col_names": aggregation_parcellation_one["aggregation"][
"col_names"
],
# Rows should be named after parcellation 2
"row_names": aggregation_parcellation_two["col_names"],
"row_names": aggregation_parcellation_two["aggregation"][
"col_names"
],
},
}
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