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Oct 16, 2012  01:10 PM | Peter Donhauser
t1_preprocess failed
Hi,

I'm running the NIAK preprocessing pipeline (niak-0.6.4.1) on a Linux machine at the BIC. t1_preprocess keeps failing at the Non-Uniformity correction step, I've attached the log-file below. I have tried to run 'nu_correct' from a Terminal with the same inputs and it works perfecly fine from there.
Any ideas?

Thanks a lot,
Peter


********************
The job starts now !
********************
***********************************
Preprocessing of a T1 brain volume
***********************************
Original brain volume : /dagher/dagher4/peterd/data/minc/subject3/anat/st20101119_150954dicom-0015-********_20101119150954_3_1MPRAGEADNI********s003a001.mnc

*****************************************
Non-uniformity correction on an MR volume
*****************************************
Running NU_CORRECT with the following command:
nu_correct -tmpdir /tmp/niak_tmp_t1_preprocess_subject1_969722732_gb_niak_omitted/ -distance 50 /dagher/dagher4/peterd/data/minc/subject3/anat/st20101119_150954dicom-0015-********_20101119150954_3_1MPRAGEADNI********s003a001.mnc /tmp/niak_tmp_t1_preprocess_subject1_969722732_gb_niak_omitted/vol_nu.mnc


HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 448 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 111 in H5Z_filter_deflate(): inflateInit() failed
    major: Data filters
    minor: Unable to initialize object
(from miset_coords): Can't read dataset /minc-2.0/image/0/image
About to loop, max_buffer is 4194304
About to loop, max_buffer is 4194304
/usr/local/bic/bin/volume_stats: /export01/local/matlab7a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /usr/local/bic/bin/volume_stats)
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)

ans =

     1


mv: cannot stat `/tmp/niak_tmp_t1_preprocess_subject1_969722732_gb_niak_omitted/vol_nu.mnc': No such file or directory

*****************
Masking the brain
*****************
Reading T1 image /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_nuc_nativet1.mnc ...


********************
Something went bad ... the job has FAILED !
The last error message occured was :
Error using ==> niak_read_vol at 180
Couldn't find any file fitting the description /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_nuc_nativet1.mnc

File /data/aces/aces1/pbellec/public/niak-0.6.4.1/commands/read_write/niak_read_vol.m at line 180
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/bricks/t1_processing/niak_brick_mask_brain_t1.m at line 234
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/bricks/t1_processing/niak_brick_t1_preprocess.m at line 437
File /data/aces/aces1/pbellec/public/psom-dev/psom_run_job.m at line 110

****************
Checking outputs
****************
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/transf_subject1_nativet1_to_stereolin.xfm has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/transf_subject1_stereolin_to_stereonl.xfm has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/transf_subject1_stereolin_to_stereonl_grid.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_nuc_nativet1.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_nuc_stereolin.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_nuc_stereonl.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_mask_stereolin.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_mask_stereonl.mnc has not been generated!
The output file or directory /dagher/dagher4/peterd/data/fmri_preprocess_rest/anat/subject1/anat_subject1_classify_stereolin.mnc has not been generated!

**********************************************
16-Oct-2012 15:20:01 : The job has FAILED
Total time used to process the job : 0.28 sec.
**********************************************

ans =

     1