Control script for running resting-state pipe

Description: This script imports a set of python modules to be used
for processing fMRI BOLD connecitivity data from the UCSF Neuroimaging Center and 
the UCSF Memory and Aging Center. The script should be run on the cloud at:
/mnt/macdata/groups/Rest_Pipe/. If you drop your data in that directory
and call the fallowing commands, this script will run: 

1.) Dicom to niftii conversion (dcm2nii)
2.) Skull stripping (FSL BET)
3.) Realigning the EPIs to the first aquisition in EPI sequence.(SPM)
4.) Register Ac-Pc aligned T2 weighted image to EPIs (SPM)
5.) Run distortion correction using T2 image (MATLAB, ITK)
6.) Register your EPIs to an Ac-Pc aligned T1 (SPM)
7.) Run Partial Volume Correction (MATLAB)
8.) Normalize EPIs to MNI 152 space (SPM)
9.) Extract a BOLD time series from MNI defined ROIs (FSL)
10.) Filter the time-series at 0.08 - 0.1Hz (Matlab)
11.) Run pairwise partial-corellations between all ROIs.(Matlab)
12.) Run a GLM for specific seed ROIs (DMN, Motor, Language), include motion, GMWM, Ventricles as regressors (Matlab)
13.) Correct for multiple comparisons using a surrogate simulation (MATLAB)

Dependencies: Matlab, Python 2.7 >, Nipype, SPM, FSL, Freesurfer, ITK