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notesAboutSettingUp.txt
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notesAboutSettingUp.txt
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Stemp -1:
a. Install appropriate version of Rails & gems (see config/environment.rb for which versions to install)
b. Make sure that rubygems itself is pre-2.0:
gem update --system 1.8.25
If you're running a version of Ruby > 1.9.3-p350 or so, you'll need to downgrade gems like this or else you'll see the "undefined method source_index" error.
Step 0. Generate nii.gz of dcm files.(using Slicer or dcm2nii or mriconvert) Verify using ITK-SNAP
Step 1. Add Template study:
RAILS_ENV='production' ruby script/console
ts = TemplateStudy.new(:name => 'headNeck1', :nii => File.open('/Users/jayashreekalpathy/Documents/tactics/webapp/tactics/public/headNeck1.nii.gz', 'rb'))
ts.save
TemplateStudy.find(:all).size
Also need pixel spacing, origin and slice thickness
irb
require 'dicom'
obj = DICOM::DObject.new('IM-0001-0118.dcm');
orig = obj.value("0020,0032")
pix=obj.value("0028,0030")
Create jpgs into thumbs directory
batch_convert_dcm
img = dimg.get_image_magick(:rescale => true).normalize
Step 2. Create users
check db to ensure user created
Step 3. Submit contour
upload RTSTRUCT file, check db to see if contouring session is created.
Step 4. Generate masks
RAILS_ENV='production' rake jobs:work
touch tmp/restart.txt
Step 4. Populate metrics and generate report