bugfix: error due to "ls -d" returning timeseries filenames instead of dirnames only

change "ls -d" command to ensure it gets only task-run dirnames, without also getting timeseries filenames from the Results dir. Fixes an error which occured when the first result returned by ls -d was not a task-run directory.

Fix: atlas used for Altas-in-T1 and T1-in-Atlas was incorrect

When the atlas is supplied via pipelines.py, it is now passed in to the pre-processing script correctly. The default atlas has been replaced and is correct for adult subjects.

Issue #12 fix (task image creation error on subjects w/o T2w)

Now skips T2w task image creation for subjects w/o T2w, preventing an error from occurring.

HOTFIX: atlas argument fix

Atlas argument was not being passed along in some circumstances.

Executive Summary fix for daic2hcp

daic2hcp didn't have the task-* folders at the top level of the "output" folder. They did exist however in the MNINonLinear/Results folder. Since that is consistent across pipelines we can use it for both.

Fix: Executive Summary was not finding pngs after changes in anat-only.

v2.2.5

Fix: needed to find pngs after anat-only changes.

Fix: None is a string when applied to session id.

Handling "None" passed withing Python 3 is tricky. If we do not specify the arg at all, it properly assigns the None object. But if we try to pass a None object, it passes it as a string, "None", which is very different. So, to handle paths, needed to check each object passed in for a value of "None". However, in the case of session ids, the string passed in is sometimes equal to "None" and that is a valid session id. The problem is, since Python is not passing a None object, there is no way to know if we are receiving a string containing "None" because it was a string in the caller or a string containing "None" because it was a None object in the caller. I contend this is a bug in Python. Regardless, I need to handle the session Id as if it were a string containing "None".

Executive summary should handle None for optional directories.

When processing anatomy-only subjects (no rest or other task data), pass None for the path to the BIDS functional input, and for the path to the output of such data (usually summary_DCANBoldProc...). In both cases, Executive Summary needs to handle the situation gracefully and process the data it is able to process.

Fixes to placeholders, permissions.

v2.2.1

Placeholders were the wrong shapes for new layout. Now use html to ma…

New layout

Layout the 9 slices in rows rather than blocks, so that the same slice in 2 views are next to (vertically) each other.