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binarybottle committed May 26, 2012
1 parent 5d8bbd8 commit 0c10a89011d9c9840b97d80da0376813adef5553
Showing with 7 additions and 4 deletions.
  1. +6 −3 preprocess_beebrains.py
  2. +1 −1 process_beebrains.py
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@@ -39,7 +39,10 @@
import numpy as np
from scipy.ndimage.filters import gaussian_filter
-ANTS = '/software/ANTS_1.9/bin/' # for registration (motion correction)
+#ANTS = '/software/ANTS_1.9/bin/' # for registration (motion correction)
+#IMAGEMAGICK = '/usr/local/bin/' # only if converting images and creating montage movies
+#ANTS = '/software/ANTS/bin/' # for registration (motion correction)
+ANTS = '/usr/local/bin/' # for registration (motion correction)
IMAGEMAGICK = '/usr/local/bin/' # only if converting images and creating montage movies
# Settings
@@ -48,7 +51,7 @@
frames_per_run = 232 # number of images captured for each run
# Steps to run:
-convert_images = 1 # convert .pst images to nifti file format
+convert_images = 0 # convert .pst images to nifti file format
correct_motion = 1 # apply registration to correct for motion
smooth_images = 1 # smooth the resulting motion-corrected images
@@ -66,7 +69,7 @@
# Save image types:
save_affine = 0 # Save affine transform -- NOTE: Using average of affine transforms instead
save_nonlinear = 0 # Save nonlinear transform -- NOTE: Using average of nonlinear transforms instead
-save_affine_avg = 1 # Use average of affine transformsinstead
+save_affine_avg = 1 # Use average of affine transforms instead
save_nonlinear_avg = 1 # Use average of nonlinear transforms instead
save_montages = 0 # Save for visualizing results:
save_movie = 0 # Very memory intensive -- better to use another program such as GraphicConverter
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@@ -61,7 +61,7 @@
args = sys.argv[1:]
if len(args)<2:
print("\n\t Please provide a subject string and the name of the data/output directory.")
- print("\t Example: python " + sys.argv[0] + " bk120309e.lst subject data output")
+ print("\t Example: python " + sys.argv[0] + " bk120309e.lst bk120309e.lst output")
sys.exit()
else:
subject = str(args[0]) # 'bk120309e.lst'

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