dcm2nii interface fails when compression is not possible #1267
Description
heudiconv fails to convert an SWI scan:
> /home/data/psyinf/forrest_gump/satratest/git/bin/heudiconv(305)convert()
304 else:
--> 305 shutil.copyfile(res.outputs.converted_files, outname)
306 if isdefined(res.outputs.bvecs):
ipdb> res.outputs.converted_files
<undefined>
I cannot debug this to 100% certainty right now, but my guess is that the interface doesn't detect any output, because dcm2nii stdout doesn't leave a compatible trace. Here is what it looks like (cropped to representative lines):
% dcm2nii -a y -c y -v y -d y -e y -g y -i n -n y -o /tmp/heudiconvtmpyZJZzv/convert -p y -x n -f n IM_0320 Chris Rorden's dcm2nii :: 4AUGUST2014 (Debian) 64bit BSD License
reading preferences file /home/mih/.dcm2nii/dcm2nii.ini
0 files in working directory /tmp/heudiconvtmp3Hk3fK/study_hw97swi
Data will be exported to /tmp/heudiconvtmpyZJZzv/convert/
Validating 1002 potential DICOM images.
Found 1000 DICOM images.
Converting 1000/1000 volumes: 2
IM_0501->20140909_100509VENBOLDHR32chSHCSENSEs301a1003.nii
Warning: images have different precision or intensity scaling - saving as 32-bit float
Very large volume: 0.9765625 Gb: slice-by-slice conversion required.
Unable to automatically GZip such a large file.
Converting data to 32-bit float to correct for differences slope/intercept/precision: 16.04590988 0.00000000 16
Converting data to 32-bit float to correct for differences slope/intercept/precision: 16.04590988 0.00000000 16
Converting data to 32-bit float to correct for differences slope/intercept/precision: 16.04590988 0.00000000 16
...
Converting data to 32-bit float to correct for differences slope/intercept/precision: 1.53455436 -3142.00000000 16
Converting data to 32-bit float to correct for differences slope/intercept/precision: 1.53455436 -3142.00000000 16
Converting data to 32-bit float to correct for differences slope/intercept/precision: 1.53455436 -3142.00000000 16