

before running /bin/picasso.sh, you need to install the following dependencies in the system

- DRAMMS     for registration      1.4.3    (http://www.nitrc.org/projects/dramms)
- FSL        for image operations  5.0.9    (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)
- NiftySeg   for label fusion      0.9.4    (http://sourceforge.net/projects/niftyseg)
- AFNI       for image operations  16.2.06  (http://afni.nimh.nih.gov/afni/download)
- N4         for bias correction            (http://www.insight-journal.org/browse/publication/640)
- c3d        for calculating DICE  0.8.2    (http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Documentation)
- ROBEX      for skull stripping   1.2      (https://www.nitrc.org/projects/robex)
- BrainSuite for skull stripping   v.16a    (http://brainsuite.org/download/, linux version)
- FreeSurfer for skull stripping   5.3      (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)


You should have these programs installed and included in the system $PATH. To test, try all "which" commands below. If any of the "which" command below does not return a valid path, then picasso.sh will not run successfully. 
>> which dramms
>> which fslmaths
>> which bet2
>> which flirt
>> which seg_LabFusion
>> which nifti1_test
>> which 3dcalc
>> which 3dSkullStrip
>> which N4
>> which c3d
>> which bse
>> which mri_watershed
>> which runROBEX.sh

