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Generated slicewise clustering with only AD and AVF #12

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Generated slicewise clustering with only AD and AVF #12

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4 changes: 3 additions & 1 deletion scripts/clustering_slicewise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
# 7: Paxinos tract 2
# ..
# 12: Paxinos tract 7
ind_metrics = [0, 2]
logging.info("\nLoad data for level: " + level)
nii = nib.load(params.file_prefix_all + level + ext)

Expand Down Expand Up @@ -78,7 +79,8 @@

# Reshape data used for clustering
# Here, we will perform clustering on the first 5 volumes (ie: selection on the 4th dimension)
data2d = data_crop[:, :, 0, 0:5].reshape(-1, 5)

data2d = data_crop[:, :, 0, ind_metrics].reshape(-1, len(ind_metrics))

# Standardize data
logging.info("Standardize data...")
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2 changes: 1 addition & 1 deletion scripts/params.py
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Expand Up @@ -13,7 +13,7 @@
folder_processing = 'processing_temp' # Where to put intermediate processed images
folder_concat_region = 'processing_regionwise'

folder_clustering_slicewise = 'results_clustering_slicewise' # Where to put results of slicewise clustering
folder_clustering_slicewise = 'results_clustering_slicewise_AD-AVF' # Where to put results of slicewise clustering
folder_clustering_regionwise = 'results_clustering_regionwise' # Where to put results of region-wise clustering

file_prefix = 'AtlasRat_'
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