From 4f2723b2f9b054ec420163cafd6a198f68ad33aa Mon Sep 17 00:00:00 2001 From: Victor Vera Frazao Date: Tue, 12 Dec 2023 15:21:32 +0100 Subject: [PATCH] Issue #7: Deprecation bug fix. --- bin/3.3_fMRIActivity/create_seed_rois.py | 2 +- bin/3.3_fMRIActivity/fsl_mean_ts.py | 8 ++++---- bin/3.3_fMRIActivity/process_fMRI.py | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/bin/3.3_fMRIActivity/create_seed_rois.py b/bin/3.3_fMRIActivity/create_seed_rois.py index 50c7161..d4facc7 100755 --- 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 index 6fec4dc..cb80a22 100755 --- 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 index 715e7d1..4a8221f 100755 --- 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: