BIRN Deidentification and Upload Pipeline
Author: Silvester Czanner (see also: SilvesterNotes)
- Overview of anonymizing and defacing code
- Limitations of the code
- Contents in distribution
- Setting up local environment variables for use
- Use instructions
- 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