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CoBrALab / quarantine

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mincresample and hd5 files #17

Closed raihaan closed 9 years ago

raihaan commented 9 years ago

tried a basic mincresample in.mnc out.mnc on an h2f5 file and it crashed. this is in contrast with running mincresample smoothly on a netcdf file.

bug in file/file format? bug in code? due to older minc-toolkit version?

gdevenyi commented 9 years ago

Where's my logfiles?

raihaan commented 9 years ago

patrai@cicws23:/data/chamal/projects/raihaan/rai_eric/input/subjects/brains$ mincresample CTGlu_ConGlu001_t1.mnc /tmp/resampletest.mnc Transforming slices:HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:

000: H5Dio.c line 182 in H5Dread(): can't read data

major: Dataset
minor: Read failed

001: H5Dio.c line 550 in H5D__read(): can't read data

major: Dataset
minor: Read failed

002: H5Dchunk.c line 1837 in H5D__chunk_read(): unable to read raw data chunk

major: Low-level I/O
minor: Read failed

003: H5Dchunk.c line 2868 in H5D__chunk_lock(): data pipeline read failed

major: Data filters
minor: Filter operation failed

004: H5Z.c line 1175 in H5Z_pipeline(): filter returned failure during read

major: Data filters
minor: Read failed

005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed

major: Data filters
minor: Unable to initialize object

(from miset_coords): Can't read dataset /minc-2.0/image/0/image ........................................................................................................................Done

raihaan commented 9 years ago

outputs /tmp/resampletest.mnc, but output file is blank

raihaan commented 9 years ago

after some investigation, discovered that mincresample runs properly for a subset of the data set. Certain files were transferred USB, others were transferred from scinet.

mincresample USBtransferfile.mnc out.mnc failed mincresample scinettransferfile.mnc out.mnc passed

Conclusion: A set of files transferred via USB were corrupted