Error if EchoNumber tag missing with multi-echo sequence

[nicholst]

Summary

While PR #345 successfully treats PD+T2 pairs as multi-echo, we now get runtime errors when such acquisitions are missing the EchoNumber tag:

*Runtime**Error**: was asked to copy X but destination already exists: Y

Using the --overwrite option eliminates the error but only leaves us with one echo.

Presently, multi echo support depends on EchoNumber tag, but given there are DICOM files in the wild that lack this tag we need a backup logic, presumably based on EchoTime. I can see that this requires a modification to the logic of save_converted_files in convert.py... something like

EchoNumberBackup = [x+1 for x in sorted(range(len(echo_times)), key=echo_times.__getitem__)]

and then assignment of echo_number will need to check for empty value and use EchoNumberBackup when missing. I can almost see what to do but it's just a bit beyond my very elementary Python.

Platform details:

Choose one:

• Local environment

Python 3.6.6

• Heudiconv version:

v0.5.4 + PR #345 patch

[yarikoptic]

another related is #346 - "Provide flexible support for multi-volume sequences" ;-)

[tsalo]

I fixed this on my fork by converting echo_times into a list and using the file's EchoTime to index that list (plus one) to get the echo number if EchoNumber wasn't in fileinfo's keys.

I.e.,

# Get the EchoNumber from json file info.  If not present, use EchoTime
if 'EchoNumber' in fileinfo.keys():
    echo_number = fileinfo['EchoNumber']
else:
    echo_number = echo_times.index(fileinfo['EchoTime']) + 1

I'd be happy to open a PR, unless there are plans for a different fix.