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FIX: Determine multi-echo echo numbers from EchoTimes #366

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merged 3 commits into from
Aug 21, 2019
Merged

FIX: Determine multi-echo echo numbers from EchoTimes #366

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e57755e
Use EchoTime when EchoNumber is unavailable.
tsalo Aug 6, 2019
c227177
Fix spacing.
tsalo Aug 7, 2019
4bc9eee
Merge remote-tracking branch 'nipy/master' into multi-echo
tsalo Aug 21, 2019
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12 changes: 7 additions & 5 deletions heudiconv/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,11 +518,11 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
# echo times for all bids_files and see if they are all the same or not.

# Check for varying echo times
echo_times = set(
echo_times = sorted(list(set(
load_json(b).get('EchoTime', None)
for b in bids_files
if b
)
)))

is_multiecho = len(echo_times) > 1

Expand Down Expand Up @@ -574,9 +574,11 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
# For multi-echo sequences, we have to specify the echo number in
# the file name:
if bids_file and is_multiecho:
# Get the EchoNumber from json file info. If not present, it's echo-1
echo_number = fileinfo.get('EchoNumber', 1)

# Get the EchoNumber from json file info. If not present, use EchoTime
if 'EchoNumber' in fileinfo.keys():
echo_number = fileinfo['EchoNumber']
else:
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We should ensure echotime is available

Suggested change
else:
elif fileinfo.get('EchoTime'):

and just set echo_number to None if neither are defined.

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I was thinking that, since this line should only be reached if the data are multi-echo, it should raise an error if EchoTime is unavailable. What was happening before (in #347) was that the real cause of the error (missing EchoNumber field) was being obscured because the value was defaulting to 1. The error I was getting there was from copying files, which was hard to interpret.

That said, maybe defaulting to None will make the resulting error clearer, while defaulting to 1 made it confusing.

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Either way is fine to me - let's keep it as you have it. Could you merge with master - the CI problem should be fixed now

echo_number = echo_times.index(fileinfo['EchoTime']) + 1

supported_multiecho = ['_bold', '_epi', '_sbref', '_T1w', '_PDT2']
# Now, decide where to insert it.
Expand Down