= BIRN Deidentification and Upload Pipeline =

''Author: Silvester Czanner (see also: SilvesterNotes)''
----
 
 1. Overview of anonymizing and defacing code
 2. Limitations of the code
 3. Contents in distribution
 4. Setting up local environment variables for use
 5. Use instructions
 6. Support and contacts
  
== 1. Overview of anonymizing and defacing code  ==

 Goal:: To anonymize and deface the dicom files
  
We provide a script (birnd_up) that reads a dicom image files,
anonymizes the dicom headers and defaces dicom image volumes.
 
== 2. Limitations of the code ==
 
 * This anonymizing and defacing code has been tested on 3D structural images acquired on Siemens (Avanto and Sonata gradients) and GE (CRM and BRM gradients) systems
 * This code has been developed for linux platforms and tested on RED HAT, Fedora Core 2
 
 To convert the dicom files to TIF images and visualy chceck the results
 *  This code needs a Matlab license and an Image Toolbox license.
 *  This code has been tested on Matlab's version 7.0 (r14)
 
== 3. Contents of distribution ==
  
The whole distribution package contains 6 subdirectories:
  || atlas                 || face.gca, talairach_mixed_with_skull.gca ||
  || matlab                || save_mgh_as_tifs.m ||
  || scripts               || birnd_up ||
  || bin                   || dccp, dcdump, dcmdump, gentodc, mri_watershed-test, tclkit, mri_deface, mri_convert ||
  || dcanon                || a2mrml, dcanon, dcanon.tcl ||
  
== 4. Setting up local environment variables ==
  
You need to set up the following two variables:
  
Setup the environment variable '''BIRND_UP_DIR''' to the BIRND-UP directory.
For example:

  ''setenv BIRND_UP_DIR /my_home_directory_path/BIRND-UP''
  
Setup the variable '''MATLAB''' to the path of your matlab executable file
For example:

  ''setenv MATLAB /space/lyon/6/pubsw/common/matlab/7.0/bin/matlab''
  
With these environments you can define aliases to run the scripts:

  ''alias birnd_up $BIRND_UP_DIR/scripts/birnd_up''
   
And then just run the scripts by typing:

  ''birnd_up  (or birnd_up -help)''
 
== 5. How to use it ==
  
 USAGE:: birnd_up [options] -i <indir> -o <outdir> -subjid <subjID>
  
 || -i indir                       ||: input directory <dcmdir> ||
 || -o outdir                      ||: output directory ||
 || -study studydir                ||: study directory ||
 || -subjid subject_ID             ||: subject ID ||
 || -radius radius                 ||: radius in [mm], default 5 ||
 || -radius distance_from_brain    ||: Default is 7mm, but if a bit of brain is being stripped, it can be increased, or if too much is face is left, it can be decreased. ||
 || -result_check                  ||: create tif images from defaced volume ||
 || -version                       ||: print version string ||
 || -help                          ||: show the usage text ||
  
=== Examples: ===
{{{
 set DATA1=/your_path/data1 
 set DATA2=/your_path/data2 
 set OUTPUT_DIR=/your_path/defaced_dicoms 
}}}
''./birnd_up -i $DATA1 $DATA2 -o $OUTPUT_DIR -subjid test_subj''
  
Defaced dicom files will be in:

||$DATA1 --> $OUTPUT_DIR/test_subj/scan_1||
||$DATA2 --> $OUTPUT_DIR/test_subj/scan_2||
 
''./birnd_up -i $DATA1 $DATA2 -o $OUTPUT_DIR -subjid test_subj -study1 visit1''
 
Defaced dicom files will be in:

||$DATA1 --> $OUTPUT_DIR/test_subj/visit1/scan_1||
||$DATA2 --> $OUTPUT_DIR/test_subj/visit1/scan_2||
  
''./birnd_up -i $DATA1 $DATA2 -o $OUTPUT_DIR -subjid test_subj -study1 visit1 -result_check''
 
Defaced dicom files will be in:

||$DATA1 --> $OUTPUT_DIR/test_subj/visit1/scan_1||
||$DATA2 --> $OUTPUT_DIR/test_subj/visit1/scan_2||
 
TIF images from defaced data will be in:

||$DATA1 --> $OUTPUT_DIR/test_subj/visit1/scan_1_tif||
||$DATA2 --> $OUTPUT_DIR/test_subj/visit1/scan_2_tif||
  
== 6. Support and contacts ==
  
Support is very limited but we will do our best to try to answer your questions.
Please email your constructive comments to:
Silvester Czanner (czanner@nmr.mgh.harvard.edu)
Karl Helmer (helmer@nmr.mgh.harvard.edu)

More information about the BIRND-UP distribution is on: http://www.na-mic.org/Wiki/index.php/MBIRN:BIRNDUP:Distribution