Mercurial > repos > greg > drmi

changeset 35:013144510199 draft

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Uploaded
author greg
date Thu, 30 Nov 2017 10:45:16 -0500
parents fd434b04f717
children 501221517d3f
files dmri.py
diffstat 1 files changed, 19 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/dmri.py	Thu Nov 30 10:45:09 2017 -0500
+++ b/dmri.py	Thu Nov 30 10:45:16 2017 -0500
@@ -4,7 +4,7 @@
 import shutil
 
 from dipy.core.gradients import gradient_table
-from dipy.data import fetch_sherbrooke_3shell, fetch_stanford_hardi, read_stanford_labels
+from dipy.data import fetch_stanford_hardi, fetch_stanford_t1, read_stanford_labels
 from dipy.io import read_bvals_bvecs
 from matplotlib import pyplot
 
@@ -35,18 +35,25 @@
 
 # Get input data.
 input_dir = args.drmi_dataset
-#if input_dir == 'stanford_hardi':
-if args.drmi_dataset_type == "dataset":
-    fetch_stanford_hardi()
-    fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
-    fbval = os.path.join(input_dir, 'HARDI150.bval')
-    fbvec = os.path.join(input_dir, 'HARDI150.bvec')
-    img = nibabel.load(fdwi)
+if input_dir == 'stanford_hardi':
+    if args.drmi_dataset_type == "dataset":
+        fetch_stanford_hardi()
+        fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
+        fbval = os.path.join(input_dir, 'HARDI150.bval')
+        fbvec = os.path.join(input_dir, 'HARDI150.bvec')
+        img = nibabel.load(fdwi)
+    else:
+        img, gtab, labels = read_stanford_labels()
+        fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
+        fbval = os.path.join(input_dir, 'HARDI150.bval')
+        fbvec = os.path.join(input_dir, 'HARDI150.bvec')
 else:
-    img, gtab, labels = read_stanford_labels()
-    fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
-    fbval = os.path.join(input_dir, 'HARDI150.bval')
-    fbvec = os.path.join(input_dir, 'HARDI150.bvec')
+    # input_dir == 'stanford_t1
+        fetch_stanford_t1()
+        fdwi = os.path.join(input_dir, 'HARDI93.nii.gz')
+        fbval = os.path.join(input_dir, 'HARDI93.bval')
+        fbvec = os.path.join(input_dir, 'HARDI93.bvec')
+        img = nibabel.load(fdwi)
 
 data = img.get_data()
 # data is a 4D array where the first 3 dimensions are the i, j,