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moloney / dcmstack

DICOM to Nifti conversion with meta data preservation
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Problematic dataset #14

Closed chrisgorgo closed 11 years ago

chrisgorgo commented 11 years ago

Quoting after @DerOrfa "dcmstack . --file-ext ".IMA" --force-read --output-name remove --output-ext ".nii" --dest-dir "/tmp/" -v --embed-meta" on it takes ages, produces an lot of messages like

/afs/cbs.mpg.de/software/pythonlib/lib/python2.7/site-packages/dcmstack-0.7.dev-py2.7.egg/dcmstack/dcmstack.py:1044: UserWarning: Error adding file ./HN3T110609.MR.RT_ANATOMY.13.189.2011.06.09.10.21.57.312500.111344242.IMA to stack: data dtype "object" not recognized (fn, str(e)))

... and eventually ends with no output.

Here's the dataset: https://dl.dropboxusercontent.com/u/412959/S13_MP2RAGE_5_3_TR5000_noGRAPPA_Inv2_PHS.tar.bz2

moloney commented 11 years ago

This is the same problem described here: https://github.com/moloney/dcmstack/pull/7

Should be fixed in the latest nibabel. For me the conversion takes about 25 seconds.

DerOrfa commented 11 years ago

The latest version works fine now. Sorry for bothering..