

PICASSO (Personalized Congregation of Algorithms for Skull Stripping Optimization)



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Intro
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PICASSO is a program for skull stripping brain MR images. Skull stripping is also known as brain extraction. The features of PICASSO include

-- fully automated
-- no need to tune parameters
-- high accuracy
-- generally applicable to brain MRIs
	(a) in multiple imaging sites; 
	(b) by scanners of various vendors (GE/Siemens/Philips); 
	(c) by scanners of various magnetic field strengths (1.0T/1.5T/3T/7T); 
	(d) by various T1-weighted pulse sequences (MPRAGE, SPGR, etc); 	
	(e) with various fields-of-view (even containing neck and shoulders);
	(f) from subjects of various ages (infants, pediatrics, young adults, elderly adults); 
	(g) from subjects of different health conditions (normative, dementia, tumor-bearing); 
	(h) with various image resolutions (from 1x1x1mm to 1.5x1.5x6mm); and 
	(i) with various image contrasts (high or low SNRs).


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Running Environment
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This program is a bash script running in the unix operating system under linux, mac or windows x-term. It can be run in a single-CPU desktop, or in distributed clusters (MOSIX, PBS or SGE).



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Dependencies
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- DRAMMS    for registration      (http://www.nitrc.org/projects/dramms)
- FSL       for image operations  (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)
- NiftySeg  for label fusion      (http://sourceforge.net/projects/niftyseg)
- AFNI      for image operations  (http://afni.nimh.nih.gov/afni/download)
- N4        for bias correction   (http://www.insight-journal.org/browse/publication/640)
- c3d       for calculating DICE  (http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Documentation)
- ROBEX     for skull stripping   (https://www.nitrc.org/projects/robex)
- bse       for skull stripping   (http://brainsuite.org/download/)

You should have these programs installed and included in the system $PATH. In
other words, the normalizeFOV.sh program should be able to find the above
programs by the 'which' command, eg.,
>> which dramms
>> which fslmaths
>> which seg_LabFusion
>> which 3dcalc
>> which N4
>> which c3d
>> which bse11a


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Usage
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No need to install. After unzip the package, there will be two sub-folders (./atlases and ./bin).
If you run the ./bin/picasso.sh program without any arguments, you will see the syntax

>> ./bin/picasso.sh


########################################
Summary: This script takes an input brain MR image (T1-weighted) and normalize
its FOV to the standard FOV defined in the MNI152 space. This script can be
run in a single linux machine or in a parallel cluster (e.g., PBS).


########################################
USAGE: $0 [OPTIONS]
OPTIONS:

Reqd:   -in      <file>     : input T1-weighted MRI (image must be in *.nii.gz format).
        -out     <file>     : output FOV mask image (in *.nii.gz format).

Optional:
        -debug              : debug mode, keep all intermediate results
        -runmode <int>      : 1 mutiple registrations run in parallel in the PBS cluster (default if PBS cluster exists);
                              2 multiple registrations run in parallel but in the same linux machine (default if PBS cluster does not exist);
                              3 multiple registrations run sequentially in the same linux machine;

########################################
Dependencies:
        FSL      < http://fsl.fmrib.ox.ac.uk/fsldownloads >
        DRAMMS   < https://www.nitrc.org/projects/dramms >   version 1.4.3 and up
        NiftiSeg < http://sourceforge.net/projects/niftyreg >


########################################
Example Use:
        ./bin/normalizeFOV.sh -in myimage.nii.gz -out myimage_FOVnormalized.nii.gz


########################################
Author:
        Yangming Ou (yangming.ou@childrens.harvard.edu),
        A.A. Martinos Center, Massachusetts General Hospital, Harvard Medical Schol
        (c) 2014-2016
	Boston Children's Hospital, Harvard Medical School
	(c) 2016-2018


########################################
Reference:
        pending.
	Y Ou, L Zöllei, X Da, K Retzepi, SN Murphy, ER Gerstner, BR Rosen, PE Grant, J Kalpathy-Cramer, RL Gollub, "Field of View Normalization in Multi-Site Brain MRI", Neuroinformatics, doi: 10.1007/s12021-018-9359-z, (2018).


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License
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BSD


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Note
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Note: Part of the PICASSO program, namely the multiatlas_skullstripping.sh,  was modified based on the mass program (Jimit Doshi, Guray Erus, Yangming Ou, Bilwaj Gaonkar, Christos Davatzikos. Multi-Atlas Skull-Stripping, MASS. Academic Radiology, software http://www.cbica.upenn.edu/sbia/software/MASS/index.html).

The original author for that part (multiatlas_skullstripping.sh) was Jimit Doshi from the University of Pennsylvania.

Modifications were done by Yangming Ou in 2014-2015 while working at MGH.

Modifications were allowed by MASS' license given that the modified version is not used for any commercial purpose. Therefore, PICASSO is only free for academic use. 




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Contact: Yangming Ou (yangming.ou@childrens.harvard.edu)


copyright 2014-2018
Massachusetts General Hospital
Boston Children's Hospital
Harvard Medical School


