Issue #7: Deprecation bug fix.

Aswendt-Lab · Dec 12, 2023 · 4f2723b · 4f2723b
1 parent cd0c5ad
commit 4f2723b
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/bin/3.3_fMRIActivity/create_seed_rois.py b/bin/3.3_fMRIActivity/create_seed_rois.py
@@ -67,7 +67,7 @@ def startSeedPoint(in_labels,in_atlas):
         labels_data.append(labels_img[k].get_data())
         # print("labels_data[%d].dtype:" % (k,), labels_data[k].dtype)
         # print("labels_data[%d].shape:" % (k,), labels_data[k].shape)
-        labels_hdr.append(labels_img[k].get_header())
+        labels_hdr.append(labels_img[k].header)
         labels_shape.append(labels_hdr[k].get_data_shape())
         # print("labels_shape[%d]:" % (k,), labels_shape[k])
         if len(labels_shape[k]) != 3:

diff --git a/bin/3.3_fMRIActivity/fsl_mean_ts.py b/bin/3.3_fMRIActivity/fsl_mean_ts.py
@@ -23,7 +23,7 @@ def start_fsl_mean_ts(sPathData,sPathMask,labelNames,postTxt):
     # Read 4D data file (NIfTI )
     data_img = nib.load(sPathData)
     data = data_img.get_data()
-    data_hdr = data_img.get_header()
+    data_hdr = data_img.header
     data_dtype = data_hdr.get_data_dtype()
     data_shape = data_hdr.get_data_shape()
 
@@ -41,7 +41,7 @@ def start_fsl_mean_ts(sPathData,sPathMask,labelNames,postTxt):
     # Read 4D mask file (NIfTI)
     mask_img = nib.load(sPathMask)
     mask = mask_img.get_data()
-    mask_hdr = mask_img.get_header()
+    mask_hdr = mask_img.header
     #mask_dtype = mask_hdr.get_data_dtype()
     mask_shape = mask_hdr.get_data_shape()
 
@@ -114,7 +114,7 @@ def get_date():
     #data = np.cast[np.float32](data_img.get_data())
     #print("data.dtype:", data.dtype)
     #print("data.shape:", data.shape)
-    data_hdr = data_img.get_header()
+    data_hdr = data_img.header
     data_dtype = data_hdr.get_data_dtype()
     data_shape = data_hdr.get_data_shape()
     #print("data_dtype:", data_dtype)
@@ -130,7 +130,7 @@ def get_date():
     #mask = np.cast[np.float32](mask_img.get_data())
     #print("mask.dtype:", mask.dtype)
     #print("mask.shape:", mask.shape)
-    mask_hdr = mask_img.get_header()
+    mask_hdr = mask_img.header
     mask_dtype = mask_hdr.get_data_dtype()
     mask_shape = mask_hdr.get_data_shape()
     #print("mask_dtype:", mask_dtype)

diff --git a/bin/3.3_fMRIActivity/process_fMRI.py b/bin/3.3_fMRIActivity/process_fMRI.py
@@ -45,7 +45,7 @@ def imgScaleResize(img):
 
 def scaleBy10(input_path,inv):
     data = nii.load(input_path)
-    imgTemp = data.get_data()
+    imgTemp = data.get_fdata()
     if inv is False:
         scale = np.eye(4) * 10
         scale[3][3] = 1
@@ -76,7 +76,7 @@ def findSlicesData(path,pre):
 
 def getRASorientation(file_name,proc_Path):
     file_data = nii.load(file_name)
-    imgData = file_data.get_data()
+    imgData = file_data.get_fdata()
     imgData = np.flip(imgData, 2)
 
     imgData = np.flip(imgData, 0)
@@ -177,7 +177,7 @@ def copyRawPhysioData(file_name,i32_Path):
     studyName = file_name.split('/')[-3]
     scanNo = file_name.split('.')[-4]+'.I32'
     physioPath=os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(file_name))),'Physio',studyName)
-
+    print(physioPath)
     relatedPhysioData = []
     fileALL = glob.glob(physioPath+'/'+studyName+'*'+scanNo)
     for filename in fileALL: