update code for beta version

fivebillionmph · Nov 16, 2018 · bb594bb · bb594bb
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Yannan/.DS_Store b/Yannan/.DS_Store
diff --git a/Yannan/ECoG_Channel_Plotting.py b/Yannan/ECoG_Channel_Plotting.py
diff --git a/Yannan/EEG_Channel_Plotting.py b/Yannan/EEG_Channel_Plotting.py
diff --git a/Yannan/Skull-stripping.py b/Yannan/Skull-stripping.py
@@ -0,0 +1,12 @@
+#Course Name: BE 223A 18Fall 
+#Author Name: Yannan Lin
+#Purpose: Skull-stripping through BrainSuite
+
+#run brainsuite to get skull-stripped mr data
+import os
+
+#os.system(path of cortical_extraction.sh space path of mr data file)
+os.system("/Applications/BrainSuite18a/bin/cortical_extraction.sh /Users/yannanlin/Desktop/T1.nii.gz")
+
+#output file same path as filename.nii
+
diff --git a/Yannan/Skull-stripping_ECoG.py b/Yannan/Skull-stripping_ECoG.py
diff --git a/Yannan/Skull-stripping_EEG.py b/Yannan/Skull-stripping_EEG.py
diff --git a/Yannan/readme.md b/Yannan/readme.md
@@ -1,37 +1,24 @@
-## Skull-stripping and Channel Plotting
+## Skull-stripping 
 
-#### Components:
-- Skull-stripping_EEG.py
-- Skull-stripping_ECoG.py
-- EEG_Channel_Plotting.py
-- ECoG_Channel_Plotting.py
-
-#### Inputs:
-- Skull-stripping
- - File: MR Image data file
- - File format: NIfTI 
-- Channel plotting 
- - File: Coordinates of electrodes
- - File format: Excel
+#### Input
+- MR Image data file
+- File format: NIfTI 
 
-#### Outputs:
-- Skull-stripping
- - Skull-stripped NIfTI file
-- Channel plotting
- - Brain mask with electrodes on the surface
+#### Output
+- Skull-stripped NIfTI file
 
 #### Language:
 - Python 2.7
 
 #### Required Python Packages
 - psycopg2
 - nibabel
-- mayavi
 - xlrd
 - os
 
 #### Requried Software
 - BrainSuite 18a
 
 #### Additional Notes
-- Once Skull-stripping_EEG.py or Skull_stripping_ECoG.py runs, it will take more than 5 minutes to finish as skull-stripping through BrainSuite can take up to 20 minutes depending on the input file. During skull-stripping, a handful of files will be generated and the only one will be used for channel plotting is filename_cerebrum.mask.nii.gz. This file will generate shortly (usually less than one minute) after running the python script. 
+- Once BrainSuite runs, it will take more than 5 minutes to finish as skull-stripping through BrainSuite can take up to 20 minutes depending on the input file. During skull-stripping, a handful of files will be generated and the only one will be used for channel plotting is filename_cerebrum.mask.nii.gz. This file will generate shortly (usually less than one minute) after running the python script. 
+- EEG electrode coordinates also need to be uploaded to database beforehand.