Change hard-coded paths to getenv() for pipeline portability

[eebrown]

To help run the pipeline on other systems, I replaced hard-coded paths with environment variables. The following new environment variables must be set (with the formerly hard-coded directories as example):

setenv('ARCHIVE_DIR', '~/vsshp.net/Research/Neurotiede/aivo/archive');
setenv('FS_FINAL_DIR', '~/vsshp.net/Research/Neurotiede/aivo/FreeSurfer');
setenv('FS_TEMP_DIR', '/scratch/shared/megapet/FreeSurfer_temp');
setenv('SPM_DIR', '/scratch/shared/toolbox/spm12'); 

In addition to the environment variables previously required (DATA_DIR, MRI_DIR, MAGIA_PATH, MAGIA_ARCHIVE).

[tkkarjal]

Looks good, thanks! Merged.