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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 (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/)


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




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Usage
---------------------

No need to install. After unzip the package, there will be two sub-folders (./data and ./bin).
Run the ./bin/normalizeFOV.sh program without any arguments, you will see the syntax

>> ./bin/normalizeFOV.sh


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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@mgh.harvard.edu),
        A.A. Martinos Center, Massachusetts General Hospital, Harvard Medical Schol
        (c) 2014-2015


########################################
Reference:
        pending.
	


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License
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BSD



copyright 2014-2015
Massachusetts General Hospital
Harvard Medical School


