refactored tool chain setup, able to debug and run from vscode nowHEADmaster

4 files changed, 473 insertions, 0 deletions

diff --git a/OASIS/docs/convert.py b/OASIS/docs/convert.py
new file mode 100644
index 0000000..a210088
--- /dev/null
+++ b/OASIS/docs/convert.py
@@ -0,0 +1,18 @@
+import subprocess

+import os

+

+# path to the folder containing the images

+folder_path = "/mnt/c/Users/eric/Desktop/FSEG/DPOS/"

+

+# loop through all files in the folder

+for filename in os.listdir(folder_path):

+    # check if the file is a .gif image

+	# construct the full path to the image file

+	image_path = os.path.join(folder_path, filename)

+	

+	# construct the new file name, replacing .gif with .jpg

+	new_filename = os.path.splitext(filename)[0] + ".jpg"

+	new_image_path = os.path.join(folder_path, new_filename)

+	

+	# call the convert command from ImageMagick

+	subprocess.run(["convert", image_path, new_image_path])

diff --git a/OASIS/docs/convert_bmp.py b/OASIS/docs/convert_bmp.py
new file mode 100644
index 0000000..05de100
--- /dev/null
+++ b/OASIS/docs/convert_bmp.py
@@ -0,0 +1,18 @@
+from PIL import Image
+import os
+
+jpeg_folder = "/mnt/c/Users/eric/Documents/repos/URA/OASIS/JPEG/DPOS"
+bmp_folder = "/mnt/c/Users/eric/Documents/repos/URA/OASIS/BMP/DPOS"
+
+# Create the BMP folder if it doesn't exist
+if not os.path.exists(bmp_folder):
+    os.makedirs(bmp_folder)
+
+# Loop over all the JPEG files in the folder
+for file in os.listdir(jpeg_folder):
+    if file.endswith(".jpg"):
+        # Load the JPEG file and convert it to BMP format
+        jpeg_file = os.path.join(jpeg_folder, file)
+        bmp_file = os.path.join(bmp_folder, os.path.splitext(file)[0] + ".bmp")
+        with Image.open(jpeg_file) as im:
+            im.convert("L").save(bmp_file)
\ No newline at end of file
diff --git a/OASIS/docs/oasis_cross-sectional.csv b/OASIS/docs/oasis_cross-sectional.csv
new file mode 100644
index 0000000..9ba2029
--- /dev/null
+++ b/OASIS/docs/oasis_cross-sectional.csv
@@ -0,0 +1,437 @@
+ID,M/F,Hand,Age,Educ,SES,MMSE,CDR,eTIV,nWBV,ASF,Delay

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+OAS1_0006_MR1,F,R,24,,,,,1131,0.862,1.551,N/A

+OAS1_0007_MR1,M,R,21,,,,,1516,0.83,1.157,N/A

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+OAS1_0016_MR1,M,R,82,2,4,27,0.5,1477,0.739,1.188,N/A

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+OAS1_0199_MR1,M,R,69,5,1,30,0,1601,0.784,1.096,N/A

+OAS1_0200_MR1,F,R,60,2,4,30,0,1366,0.807,1.285,N/A

+OAS1_0201_MR1,F,R,85,4,1,26,0,1460,0.754,1.202,N/A

+OAS1_0202_MR1,F,R,23,,,,,1574,0.865,1.115,N/A

+OAS1_0202_MR2,F,R,23,,,,,1548,0.861,1.134,21

+OAS1_0203_MR1,F,R,71,2,3,30,0,1360,0.779,1.291,N/A

+OAS1_0204_MR1,M,R,48,4,1,29,0,1430,0.797,1.227,N/A

+OAS1_0205_MR1,M,R,75,4,1,30,0.5,1891,0.716,0.928,N/A

+OAS1_0206_MR1,F,R,78,5,1,30,0,1243,0.747,1.412,N/A

+OAS1_0207_MR1,M,R,51,5,2,29,0,1714,0.819,1.024,N/A

+OAS1_0208_MR1,F,R,55,5,1,29,0,1368,0.823,1.283,N/A

+OAS1_0209_MR1,F,R,22,,,,,1328,0.842,1.321,N/A

+OAS1_0210_MR1,F,R,73,4,1,28,0.5,1676,0.722,1.047,N/A

+OAS1_0211_MR1,M,R,20,,,,,1657,0.849,1.059,N/A

+OAS1_0212_MR1,F,R,74,3,,28,0,1614,0.697,1.087,N/A

+OAS1_0213_MR1,F,R,48,,,,,1332,0.801,1.318,N/A

+OAS1_0214_MR1,M,R,18,,,,,1854,0.87,0.947,N/A

+OAS1_0216_MR1,F,R,71,4,3,30,0,1503,0.792,1.168,N/A

+OAS1_0217_MR1,F,R,78,4,3,27,0.5,1393,0.692,1.26,N/A

+OAS1_0218_MR1,F,R,26,,,,,1291,0.843,1.36,N/A

+OAS1_0220_MR1,F,R,75,5,1,30,0,1317,0.742,1.332,N/A

+OAS1_0221_MR1,F,R,94,5,1,29,0,1474,0.696,1.19,N/A

+OAS1_0222_MR1,F,R,49,,,,,1164,0.805,1.508,N/A

+OAS1_0223_MR1,M,R,84,2,,20,1,1641,0.703,1.07,N/A

+OAS1_0224_MR1,F,R,22,,,,,1378,0.852,1.274,N/A

+OAS1_0226_MR1,M,R,90,1,4,23,0.5,1668,0.644,1.052,N/A

+OAS1_0227_MR1,F,R,26,,,,,1288,0.777,1.362,N/A

+OAS1_0228_MR1,F,R,81,3,2,28,0,1486,0.759,1.181,N/A

+OAS1_0229_MR1,F,R,55,3,3,30,0,1327,0.832,1.323,N/A

+OAS1_0230_MR1,F,R,19,,,,,1584,0.846,1.108,N/A

+OAS1_0230_MR2,F,R,19,,,,,1577,0.849,1.113,24

+OAS1_0231_MR1,F,R,20,,,,,1429,0.852,1.228,N/A

+OAS1_0232_MR1,M,R,22,,,,,1582,0.857,1.11,N/A

+OAS1_0233_MR1,F,R,77,1,4,20,0.5,1376,0.701,1.275,N/A

+OAS1_0234_MR1,M,R,75,5,2,29,0,1534,0.771,1.144,N/A

+OAS1_0235_MR1,M,R,37,,,,,1407,0.842,1.247,N/A

+OAS1_0236_MR1,F,R,20,,,,,1218,0.876,1.441,N/A

+OAS1_0236_MR2,F,R,20,,,,,1222,0.872,1.436,3

+OAS1_0237_MR1,F,R,72,2,2,27,0,1322,0.764,1.328,N/A

+OAS1_0238_MR1,F,R,77,2,3,28,0.5,1484,0.786,1.182,N/A

+OAS1_0239_MR1,F,R,29,,,,,1439,0.823,1.22,N/A

+OAS1_0239_MR2,F,R,29,,,,,1438,0.822,1.221,40

+OAS1_0240_MR1,F,R,74,2,,26,0.5,1171,0.736,1.499,N/A

+OAS1_0241_MR1,F,R,74,5,2,30,0,1400,0.754,1.254,N/A

+OAS1_0243_MR1,M,R,64,5,2,22,0.5,1547,0.742,1.134,N/A

+OAS1_0244_MR1,F,R,80,4,2,29,0,1341,0.737,1.309,N/A

+OAS1_0246_MR1,F,R,22,,,,,1522,0.841,1.153,N/A

+OAS1_0247_MR1,M,R,90,2,3,21,0.5,1307,0.689,1.342,N/A

+OAS1_0249_MR1,F,R,28,,,,,1217,0.871,1.443,N/A

+OAS1_0249_MR2,F,R,28,,,,,1215,0.865,1.444,3

+OAS1_0250_MR1,M,R,21,,,,,1500,0.837,1.17,N/A

+OAS1_0253_MR1,F,R,20,,,,,1751,0.852,1.002,N/A

+OAS1_0254_MR1,F,R,85,5,1,29,0,1264,0.705,1.388,N/A

+OAS1_0255_MR1,F,R,71,5,1,30,0,1426,0.737,1.231,N/A

+OAS1_0256_MR1,M,R,70,5,1,30,0,1660,0.739,1.057,N/A

+OAS1_0258_MR1,F,R,21,,,,,1516,0.87,1.158,N/A

+OAS1_0259_MR1,F,R,78,3,2,29,0,1334,0.773,1.316,N/A

+OAS1_0260_MR1,M,R,87,2,4,30,0,1762,0.719,0.996,N/A

+OAS1_0261_MR1,M,R,28,,,,,1417,0.845,1.238,N/A

+OAS1_0262_MR1,M,R,46,2,3,30,0,1604,0.784,1.094,N/A

+OAS1_0263_MR1,M,R,79,4,1,30,0.5,1722,0.709,1.019,N/A

+OAS1_0264_MR1,M,R,24,,,,,1591,0.849,1.103,N/A

+OAS1_0265_MR1,F,R,54,,,,,1410,0.813,1.245,N/A

+OAS1_0266_MR1,M,R,51,5,1,30,0,1793,0.834,0.979,N/A

+OAS1_0267_MR1,M,R,80,5,2,28,0.5,1506,0.679,1.166,N/A

+OAS1_0268_MR1,M,R,78,2,3,23,1,1491,0.715,1.177,N/A

+OAS1_0269_MR1,F,R,72,1,4,21,1,1489,0.683,1.179,N/A

+OAS1_0270_MR1,F,R,93,3,2,30,0,1272,0.703,1.38,N/A

+OAS1_0271_MR1,F,R,89,2,4,27,0,1329,0.74,1.32,N/A

+OAS1_0272_MR1,F,R,75,3,2,26,0.5,1355,0.745,1.296,N/A

+OAS1_0273_MR1,F,R,89,1,4,18,0.5,1480,0.676,1.186,N/A

+OAS1_0274_MR1,F,R,58,3,3,30,0,1373,0.815,1.278,N/A

+OAS1_0275_MR1,M,R,50,,,,,1635,0.802,1.073,N/A

+OAS1_0277_MR1,M,R,22,,,,,1913,0.841,0.917,N/A

+OAS1_0278_MR1,F,R,96,5,1,26,1,1465,0.684,1.198,N/A

+OAS1_0279_MR1,F,R,73,1,4,30,0,1475,0.721,1.19,N/A

+OAS1_0280_MR1,F,R,78,5,1,30,0,1440,0.67,1.219,N/A

+OAS1_0281_MR1,M,R,28,,,,,1538,0.835,1.141,N/A

+OAS1_0282_MR1,F,R,45,,,,,1478,0.819,1.188,N/A

+OAS1_0283_MR1,F,R,18,,,,,1578,0.836,1.112,N/A

+OAS1_0284_MR1,F,R,91,5,2,30,0,1714,0.746,1.024,N/A

+OAS1_0285_MR1,M,R,20,,,,,1470,0.843,1.194,N/A

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+OAS1_0286_MR1,F,R,83,3,2,20,0.5,1476,0.751,1.189,N/A

+OAS1_0287_MR1,F,R,78,3,3,21,0.5,1194,0.694,1.47,N/A

+OAS1_0288_MR1,M,R,71,2,4,20,0.5,1461,0.727,1.202,N/A

+OAS1_0289_MR1,F,R,59,3,2,28,0,1334,0.767,1.316,N/A

+OAS1_0290_MR1,M,R,83,3,2,26,0.5,1992,0.706,0.881,N/A

+OAS1_0291_MR1,F,R,73,2,2,19,1,1274,0.745,1.377,N/A

+OAS1_0292_MR1,F,R,64,4,2,30,0,1415,0.766,1.24,N/A

+OAS1_0293_MR1,F,R,69,1,2,26,0,1384,0.783,1.268,N/A

+OAS1_0294_MR1,F,R,20,,,,,1439,0.841,1.22,N/A

+OAS1_0295_MR1,F,R,20,,,,,1412,0.803,1.243,N/A

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+OAS1_0298_MR1,F,R,72,4,3,24,0.5,1354,0.738,1.296,N/A

+OAS1_0299_MR1,F,R,90,2,3,29,0,1475,0.671,1.19,N/A

+OAS1_0300_MR1,M,R,68,3,2,30,0.5,1556,0.723,1.128,N/A

+OAS1_0301_MR1,F,R,90,3,2,28,0,1495,0.761,1.174,N/A

+OAS1_0302_MR1,M,R,22,,,,,1570,0.831,1.118,N/A

+OAS1_0303_MR1,F,R,67,2,4,30,0,1221,0.831,1.438,N/A

+OAS1_0304_MR1,M,R,84,3,3,29,0.5,1497,0.693,1.172,N/A

+OAS1_0305_MR1,M,R,48,,,,,1454,0.85,1.207,N/A

+OAS1_0307_MR1,M,R,67,4,2,23,0.5,1399,0.735,1.255,N/A

+OAS1_0308_MR1,F,R,78,3,3,15,2,1401,0.703,1.253,N/A

+OAS1_0309_MR1,F,R,54,2,2,30,0,1441,0.786,1.218,N/A

+OAS1_0310_MR1,F,R,20,,,,,1388,0.863,1.265,N/A

+OAS1_0311_MR1,F,R,22,,,,,1366,0.83,1.285,N/A

+OAS1_0312_MR1,F,R,73,3,,26,0.5,1311,0.756,1.339,N/A

+OAS1_0313_MR1,F,R,20,,,,,1516,0.838,1.158,N/A

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+OAS1_0315_MR1,M,R,77,5,1,25,0.5,1604,0.773,1.094,N/A

+OAS1_0316_MR1,F,R,72,4,2,22,1,1493,0.69,1.176,N/A

+OAS1_0317_MR1,M,R,86,4,1,26,0,1501,0.702,1.169,N/A

+OAS1_0318_MR1,M,R,33,,,,,1634,0.836,1.074,N/A

+OAS1_0319_MR1,M,R,31,,,,,1527,0.821,1.149,N/A

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+OAS1_0322_MR1,F,R,65,3,4,29,0,1335,0.776,1.315,N/A

+OAS1_0323_MR1,F,R,50,5,1,30,0,1370,0.826,1.281,N/A

+OAS1_0325_MR1,F,R,27,,,,,1422,0.869,1.234,N/A

+OAS1_0326_MR1,F,R,73,3,4,29,0,1272,0.7,1.38,N/A

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+OAS1_0328_MR1,M,R,19,,,,,1453,0.878,1.208,N/A

+OAS1_0329_MR1,F,R,80,2,3,29,0.5,1209,0.76,1.451,N/A

+OAS1_0330_MR1,F,R,80,1,5,27,0,1381,0.752,1.27,N/A

+OAS1_0331_MR1,F,R,54,,,,,1467,0.821,1.196,N/A

+OAS1_0332_MR1,M,R,72,1,3,29,0,1734,0.762,1.012,N/A

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+OAS1_0335_MR1,F,R,80,1,4,27,0.5,1654,0.678,1.061,N/A

+OAS1_0336_MR1,F,R,41,,,,,1528,0.852,1.149,N/A

+OAS1_0337_MR1,M,R,81,1,4,28,0,1750,0.676,1.003,N/A

+OAS1_0338_MR1,M,R,77,4,1,29,0,1818,0.736,0.965,N/A

+OAS1_0339_MR1,F,R,79,2,,24,0.5,1211,0.694,1.449,N/A

+OAS1_0340_MR1,M,R,19,,,,,1650,0.853,1.063,N/A

+OAS1_0341_MR1,F,R,71,2,4,30,0,1479,0.772,1.187,N/A

+OAS1_0342_MR1,F,R,88,2,3,28,0,1370,0.765,1.281,N/A

+OAS1_0343_MR1,M,R,68,3,3,30,0,1441,0.811,1.217,N/A

+OAS1_0344_MR1,M,R,20,,,,,1510,0.851,1.163,N/A

+OAS1_0345_MR1,F,R,54,4,2,30,0,1389,0.831,1.264,N/A

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+OAS1_0349_MR1,F,R,43,,,,,1227,0.858,1.43,N/A

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+OAS1_0351_MR1,M,R,86,1,4,15,2,1512,0.665,1.161,N/A

+OAS1_0352_MR1,F,R,81,5,2,26,0.5,1174,0.743,1.495,N/A

+OAS1_0353_MR1,M,R,22,,,,,1680,0.8,1.044,N/A

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+OAS1_0354_MR1,M,R,74,1,3,26,0,1367,0.776,1.284,N/A

+OAS1_0355_MR1,F,R,73,4,2,29,0,1123,0.79,1.563,N/A

+OAS1_0356_MR1,F,R,68,3,2,30,0,1506,0.74,1.165,N/A

+OAS1_0357_MR1,F,R,55,4,3,30,0,1450,0.82,1.21,N/A

+OAS1_0358_MR1,M,R,65,3,3,29,0,1362,0.839,1.289,N/A

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+OAS1_0363_MR1,M,R,87,4,2,30,0,1398,0.702,1.255,N/A

+OAS1_0365_MR1,M,R,74,5,2,30,0,1806,0.754,0.972,N/A

+OAS1_0366_MR1,F,R,45,5,2,29,0,1549,0.813,1.133,N/A

+OAS1_0367_MR1,F,R,46,2,2,28,0,1161,0.841,1.511,N/A

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+OAS1_0369_MR1,F,R,73,4,1,28,0,1295,0.772,1.356,N/A

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+OAS1_0371_MR1,F,R,70,3,4,30,0,1361,0.783,1.29,N/A

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+OAS1_0373_MR1,F,R,80,3,2,20,1,1732,0.692,1.013,N/A

+OAS1_0374_MR1,F,R,73,3,3,29,0.5,1238,0.76,1.418,N/A

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+OAS1_0381_MR1,M,R,59,4,2,29,0,1795,0.809,0.978,N/A

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+OAS1_0383_MR1,M,R,58,,,,,1590,0.746,1.104,N/A

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+OAS1_0386_MR1,F,R,26,,,,,1490,0.838,1.178,N/A

+OAS1_0387_MR1,F,R,26,,,,,1149,0.851,1.527,N/A

+OAS1_0388_MR1,F,R,77,2,4,22,1,1350,0.736,1.3,N/A

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+OAS1_0390_MR1,M,R,69,2,2,24,0.5,1480,0.794,1.186,N/A

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+OAS1_0394_MR1,F,R,22,,,,,1343,0.847,1.307,N/A

+OAS1_0395_MR1,F,R,26,,,,,1295,0.834,1.356,N/A

+OAS1_0395_MR2,F,R,26,,,,,1283,0.834,1.368,39

+OAS1_0396_MR1,M,R,25,,,,,1674,0.832,1.048,N/A

+OAS1_0397_MR1,F,R,20,,,,,1265,0.846,1.387,N/A

+OAS1_0398_MR1,M,R,71,5,1,30,0,1769,0.716,0.992,N/A

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+OAS1_0400_MR1,F,R,92,5,1,25,0.5,1774,0.644,0.989,N/A

+OAS1_0401_MR1,F,R,54,4,3,29,0,1287,0.827,1.364,N/A

+OAS1_0402_MR1,F,R,76,3,2,30,0.5,1350,0.763,1.3,N/A

+OAS1_0403_MR1,M,R,19,,,,,1592,0.833,1.102,N/A

+OAS1_0404_MR1,F,R,73,2,2,29,0,1465,0.776,1.198,N/A

+OAS1_0405_MR1,M,R,77,5,1,23,1,1713,0.761,1.024,N/A

+OAS1_0406_MR1,F,R,25,,,,,1346,0.855,1.303,N/A

+OAS1_0407_MR1,F,R,55,,,,,1434,0.807,1.224,N/A

+OAS1_0408_MR1,F,R,22,,,,,1518,0.861,1.156,N/A

+OAS1_0409_MR1,M,R,34,,,,,1569,0.798,1.118,N/A

+OAS1_0410_MR1,F,R,23,,,,,1507,0.87,1.165,N/A

+OAS1_0411_MR1,F,R,71,5,1,29,0.5,1346,0.742,1.304,N/A

+OAS1_0413_MR1,F,R,25,,,,,1447,0.866,1.213,N/A

+OAS1_0415_MR1,F,R,21,,,,,1542,0.859,1.138,N/A

+OAS1_0416_MR1,F,R,23,,,,,1567,0.852,1.12,N/A

+OAS1_0417_MR1,F,R,30,,,,,1551,0.855,1.132,N/A

+OAS1_0418_MR1,M,R,74,5,2,28,0.5,1659,0.747,1.058,N/A

+OAS1_0419_MR1,F,R,21,,,,,1473,0.862,1.191,N/A

+OAS1_0420_MR1,F,R,22,,,,,1732,0.848,1.013,N/A

+OAS1_0421_MR1,F,R,22,,,,,1655,0.847,1.061,N/A

+OAS1_0422_MR1,F,R,69,4,3,29,0,1380,0.809,1.272,N/A

+OAS1_0423_MR1,M,R,75,2,4,28,0,1511,0.749,1.162,N/A

+OAS1_0424_MR1,M,R,75,4,1,20,1,1613,0.715,1.088,N/A

+OAS1_0425_MR1,F,R,78,1,4,23,1,1461,0.715,1.201,N/A

+OAS1_0426_MR1,F,R,82,5,2,29,0,1316,0.791,1.334,N/A

+OAS1_0428_MR1,F,R,84,4,3,28,0,1500,0.751,1.17,N/A

+OAS1_0429_MR1,F,R,45,,,,,1385,0.808,1.267,N/A

+OAS1_0430_MR1,M,R,71,4,1,17,1,1562,0.687,1.123,N/A

+OAS1_0431_MR1,F,R,22,,,,,1405,0.822,1.249,N/A

+OAS1_0432_MR1,F,R,72,2,4,26,0.5,1453,0.773,1.208,N/A

+OAS1_0433_MR1,M,R,58,4,1,27,0,1606,0.779,1.093,N/A

+OAS1_0434_MR1,F,R,50,,,,,1385,0.819,1.267,N/A

+OAS1_0435_MR1,M,R,23,,,,,1766,0.82,0.994,N/A

+OAS1_0437_MR1,F,R,22,,,,,1444,0.853,1.216,N/A

+OAS1_0438_MR1,F,R,66,5,2,29,0,1191,0.787,1.474,N/A

+OAS1_0439_MR1,M,R,21,,,,,1438,0.844,1.221,N/A

+OAS1_0440_MR1,M,R,86,1,4,27,0.5,1320,0.723,1.329,N/A

+OAS1_0441_MR1,M,R,81,5,1,29,0.5,1647,0.721,1.066,N/A

+OAS1_0442_MR1,F,R,23,,,,,1431,0.847,1.227,N/A

+OAS1_0443_MR1,F,R,52,3,3,30,0,1431,0.814,1.226,N/A

+OAS1_0444_MR1,F,R,30,,,,,1250,0.86,1.404,N/A

+OAS1_0445_MR1,F,R,90,1,2,29,0,1362,0.673,1.289,N/A

+OAS1_0446_MR1,F,R,80,2,4,30,0,1390,0.748,1.263,N/A

+OAS1_0447_MR1,F,R,92,4,1,24,0.5,1388,0.739,1.264,N/A

+OAS1_0448_MR1,F,R,22,,,,,1524,0.858,1.152,N/A

+OAS1_0449_MR1,F,R,71,3,4,29,0,1264,0.818,1.388,N/A

+OAS1_0450_MR1,M,R,19,,,,,1478,0.88,1.188,N/A

+OAS1_0451_MR1,M,R,73,5,3,27,0.5,1687,0.728,1.04,N/A

+OAS1_0452_MR1,M,R,75,1,4,22,1,1656,0.762,1.06,N/A

+OAS1_0453_MR1,F,R,70,1,4,29,0.5,1295,0.748,1.355,N/A

+OAS1_0454_MR1,F,R,73,3,2,23,0.5,1536,0.73,1.142,N/A

+OAS1_0455_MR1,F,R,61,2,4,28,0,1354,0.825,1.297,N/A

+OAS1_0456_MR1,M,R,61,5,2,30,0,1637,0.78,1.072,N/A

+OAS1_0457_MR1,F,R,62,3,3,26,0,1372,0.766,1.279,N/A

diff --git a/OASIS/docs/svm_c.png b/OASIS/docs/svm_c.png
new file mode 100644
index 0000000..6a1826e
--- /dev/null
+++ b/OASIS/docs/svm_c.png