Update to cfmm-base TOF

-minor update to fix base heuristic for TOF angio

Bruker compatibility and dcm2niix hotfix (+fix typo in tag)

• upgrades to dcm2niix 2019-08-01 pre-release, using @yinglilu fork with hotfixes for dwi data
• additions to Bruker 9.4T heuristic (cfmm_bruker) to include multi-echo gre, dwi, and mp2rage (based on ex-vivo cat brain protocol)

update to latest heudiconv, validator, and clean tsv

• Updated heudiconv version to v0.5.4
• Updated bids-validator version to 1.2.5
• Added clean-up of scans.tsv and events.tsv files to remove extra cols

Fix for dealing with multi-echo EPI BIDS filenames

Add scripts to correct filename errors for multi-echo EPI data. Heudiconv randomly assigns echo numbers to BIDS filenames, which do not correspond to the correct EchoNumber in the corresponding .json file. The scripts assign the correct EchoNumber to the correct EPI file and code the echo number in correct BIDS format in the filename.

Fix for dealing with multiple tar files of same subject

Merge pull request #4 from khanlab/extra_ses_bug

Fix for dealing with multiple tar files of same subject

defacing option, upgraded dependencies

• added option for defacing (-D, disabled by default)
  • uses single T1w image (first alphanumeric match of _T1w) to deface with pydeface
  • applies it to any images in anat/ with the same FOV
  • backs-up images without defacing in sourcedata/no_defaced
  • TO DO: enable defacing of other filetypes if desired
• added "--overwrite" option as default for heudiconv, so heuristic doesn't fail when duplicates encountered
• Dockerfile now contains lines for setting heudiconv, bids-validator, and pydeface versions
  • currently: heudiconv=v0.5.3, validator=1.1.3, pydeface=v1.1.0
• added flirt and fslorient Dockerfile dependencies from dropbox (without entire FSL install) for pydeface

build from nipy/heudiconv, removed defunct heuristic

minor update:

• build from nipy/heudiconv instead of isolovey branch (since fix for MAX_CSA exists)
• removed defunct heuristic for addiction study

known issues:

• overriding heuristic with a file that has the same name as built-in heuristic doesn't seem to work (uses built-in version, but copies the external one to the heudiconv folder)

another cfmm_base heuristic fix

v0.0.3c

fix to deal with duplicate GRE from console DIS2D processing

heuristic updates, MAX_CSA temporary fix

• various heuristic fixes required due to more stringent error checking in latest heudiconv
• fixed MAX_CSA limit bug temporarily by building off isolovey/heudiconv fork (bugfix in nibabel pending)

dockerfile updates to build dcm2niix & heudiconv

• Dockerfile updates to build dcm2niix & heudiconv
• fixed tab indentation in cfmm_base (now enforced by python3?)