fix: allow for template specification in at the input level
spm rewrites headers on these files

in some workflows, you want to use the files with the modified headers,
not resliced images. So we'll just return the in_files in the output.
See SPM doco Chapter 2: Realign FMI:
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf
enable list of list of files from slice time output

looks like the variable 'run' never gets used… perhaps a typo.

output spec needed adjustment to handle list of lists.
fix indents - nothing real
normalize can take a list of lists of files as input.
make the point of this var more clear.
"/path/to/folder/" should be treated the same way as "/path/to/folder"
mrtrix output fix
fixed abspath
Merge pull request #690 from satra/fix/inputtemplate

fix: allow for template specification in at the input level
in_files -> modified_in_files

also fixes an embarassing if clause, and sets realigned_files to in_files if jobtype is "estimate"
Merge pull request #691 from beOn/spm_preproc

spm preproc fixes and adds
Merge pull request #673 from bpinsard/enh/freesurfer

Enh/freesurfer resume
fix: doctest + white spaces
Merge pull request #692 from satra/fix/fsdoctest

fix: doctest + white spaces
Fixed permissions and some tests.
begin aFNI refactor
further cleanup
All tests pass
Further cleanup