parameter change

Danyyyel · Aug 22, 2024 · e5115d9 · e5115d9
1 parent 78c9cb3
commit e5115d9
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Showing 4 changed files with 13 additions and 11 deletions.
diff --git a/bin/2.1_T2PreProcessing/preProcessing_T2.py b/bin/2.1_T2PreProcessing/preProcessing_T2.py
@@ -53,7 +53,7 @@ def applyBET(input_file,frac,radius,vertical_gradient):
     scale[3][3] = 1
 
     # this has to be adapted in the case the output image is not RAS orientated - Siding from feet to nose
-    imgTemp = np.flip(imgTemp,2)
+    #imgTemp = np.flip(imgTemp,2)
     #imgTemp = np.flip(imgTemp,1)
     #imgTemp = np.flip(imgTemp,0)
     #imgTemp = np.rot90(imgTemp,2)
@@ -94,9 +94,9 @@ def applyBET(input_file,frac,radius,vertical_gradient):
 #default_rad  = 45
 #default_vert = 0.0
 
-default_frac = 0.2
+default_frac = 0.1
 default_rad  = 60
-default_vert = 0.21
+default_vert = 0.13
 
 if __name__ == "__main__":
     import argparse

diff --git a/bin/2.2_DTIPreProcessing/preProcessing_DTI.py b/bin/2.2_DTIPreProcessing/preProcessing_DTI.py
@@ -53,12 +53,11 @@ def applyBET(input_file: str, frac: float, radius: int, output_path: str) -> str
     imgTemp = data.get_fdata()
     scale = np.eye(4)* 10
     scale[3][3] = 1
-    imgTemp = np.flip(imgTemp, 2)
 
     # this has to be adapted in the case the output image is not RAS orientated - Siding from feet to nose
     imgTemp = np.flip(imgTemp,2)
-    #imgTemp = np.flip(imgTemp,1)
-    #imgTemp = np.flip(imgTemp,0)
+    imgTemp = np.flip(imgTemp,1)
+    imgTemp = np.flip(imgTemp,0)
     #imgTemp = np.rot90(imgTemp, 2)
 
     scaledNiiData = nii.Nifti1Image(imgTemp, data.affine * scale)

diff --git a/bin/2.3_fMRIPreProcessing/preProcessing_fMRI.py b/bin/2.3_fMRIPreProcessing/preProcessing_fMRI.py
@@ -54,7 +54,7 @@ def applyBET(input_file,frac,radius,outputPath):
 
     #imgTemp = np.flip(imgTemp, 2)
     #imgTemp = np.flip(imgTemp, 1)
-    imgTemp = np.flip(imgTemp, 0)
+    #imgTemp = np.flip(imgTemp, 0)
     #imgTemp = np.rot90(imgTemp,2)
 
     scaledNiiData = nii.Nifti1Image(imgTemp, data.affine * scale)
@@ -142,9 +142,9 @@ def cropToSmall(input_file,outputPath):
 #default_rad  = 45
 #default_vert = 0.0
 
-default_frac = 0.2
+default_frac = 0.1
 default_rad  = 60
-default_vert = 0.21
+default_vert = 0.13
 
 if __name__ == "__main__":
     import argparse

diff --git a/bin/conv2Nifti_auto.py b/bin/conv2Nifti_auto.py
@@ -430,8 +430,11 @@ def fileCopy(list_of_data, input_path):
         out_file = os.path.join(output_dir, "sub-" + subjid, "ses-" + sessid, "func", "sub-" + subjid + "_ses-" + sessid + "_EPI.json")
 
         # calculate slice timings
-        create_slice_timings(fmri_scan_method_file, scanid, out_file)
-
+        try:
+            create_slice_timings(fmri_scan_method_file, scanid, out_file)
+        except FileNotFoundError:
+            continue
+
     ## use parallel computing for a faster generation of t2maps
     mese_scan_sessions = []
     for id in mese_scan_ids: