initial commit of ImageJ script to create overlay MR / Histology images
finished generalizing for paths and files
working version of overlay_mr_pca.py and Sams MRI and path sh script to still be generalized
working overlay_mr_pca.py script and Sams ANTS sh script to still be generalized
adding more updates to scripts
adding STDIO feedback on what is going on
adding SGE template
new scripts for all of the prostate MR / US image registration to date, including moving around ADC maps, converting from DICOM to Nifti format
adding scripts to batch covert ARFI jpeg images to Nifti1 stacks and add blank spaces to Nifti1 stacks for image registration
working version of matlab function to add blank slices
added ability to handle 2 or 3 digit number of slices in filename
adding function to reslice Nifti1 stack based on specified voxel size
adding Python script to adjust canvas size and FIXED blank slice script to accomodate US cases with better logic
small scripts for extract specific Nifti1 header information for input into other scripts
updated CC MR script
adding new ImageJ script for BPH and Atrophy MR overlays
Merge branch 'ijm_overlay_bph_atrophy'
fixed CC MR shell script to not need too many user inputs
fixing issue with adding 1 blank slice when number of segmented path slides exceeds number of segmented image slices
adding all path to new MR overlay script and ImageJ macro