fix issue of deprecated get_data()

Author: Chenying Zhao

.vscode/launch.json

@@ -4,15 +4,26 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
-
         {
             "name": "Python: Current File",
             "type": "python",
             "request": "launch",
             "program": "${file}",
             "console": "integratedTerminal",
             //"env": {"PYTHONPATH": "/cbica/projects/GRMPY/miniconda3/condabin"},
-            "args": ["--group-mask-file","tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz","--cohort-file","GRMPY_convoxel_meanCBF_n209_indmask.csv","--relative-root","/home/chenying/Desktop/fixel_project/data/data_voxel_grmpy","--analysis_name","lm_fullOutputs","--input-hdf5","GRMPY_meanCBF_n209_indmask_nvoxels-0_wResults_20220504-180709.h5","--output-dir","GRMPY_meanCBF_n209_indmask_nvoxels-0_wResults_20220504-180709","--output-ext",".nii.gz"]
+            //"args": ["--group-mask-file","tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz","--cohort-file","GRMPY_convoxel_meanCBF_n209_indmask.csv","--relative-root","/home/chenying/Desktop/fixel_project/data/data_voxel_grmpy","--analysis_name","lm_fullOutputs","--input-hdf5","GRMPY_meanCBF_n209_indmask_nvoxels-0_wResults_20220504-180709.h5","--output-dir","GRMPY_meanCBF_n209_indmask_nvoxels-0_wResults_20220504-180709","--output-ext",".nii.gz"]
+            "args": [
+                "--index-file",
+                "FDC/index.mif",
+                "--directions-file",
+                "FDC/directions.mif",
+                "--cohort-file",
+                "cohort_FDC_n100.csv",
+                "--relative-root",
+                "/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/fixel_project/data/data_demo",
+                "--output-hdf5",
+                "demo_FDC_n100.h5"
+            ]
         }
     ]
 }

confixel/fixels.py

@@ -42,7 +42,7 @@ def mif_to_nifti2(mif_file):
     if not op.exists(nii_file):
         raise Exception(err)
     nifti2_img = nb.load(nii_file)
-    data = nifti2_img.get_data().squeeze()
+    data = nifti2_img.get_fdata(dtype=np.float32).squeeze()
     # ... do stuff with dirpath
     if dirpath:
         shutil.rmtree(dirpath)