[MINC-users] Installation issues - make check fails

[Harini Eavani]

Hello list-users,

I am having trouble with one of the binaries in the N3 software. make check fails on test 8 and passes successfully on the other 7 tests.

I have installed:
N3-1.11.0
EBTKS-1.6.2
MINC-2.0.12
NetCDF-4.0.1
HDF5-1.8.3

Here is the relevant portion of test.log :

Running test #8
nu_estimate_np_and_em -distance 100 -b_spline 1 -spline_subsample 2 -auto_mask -iterations 2 -stop 0.001 -shrink 2 -sharpen 0.15 0.01 -parzen  ./brain.mnc.gz /usr/tmp/do_test_10495//brain.imp -verbose
[root at cortex:/usr/local/N3-1.11.0/testing/] [2009-09-16 09:53:24] running:
  /usr/local/mni/bin/nu_estimate_np_and_em -distance 100 -b_spline 1 -spline_subsample 2 -auto_mask -iterations 2 -stop 0.001 -shrink 2 -sharpen 0.15 0.01 -parzen ./brain.mnc.gz /usr/tmp/do_test_10495//brain.imp -verbose


Uncorrected volume (input): ./brain.mnc.gz
Intensity mapping (output): /usr/tmp/do_test_10495//brain.imp

# Start of NU estimation algorithm
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincresample -clobber -verbose -nearest_neighbour -nelements 46 55 46 -step 4 4 4 ./brain.mnc.gz /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc
Transforming slices:..............................................Done
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -clamp -const2 1 1.7e+308 /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp
Processing:..............................................Done
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -zero -log /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc
Processing:..............................................Done
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /bin/rm /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincinfo -attvalue xspace:spacetype -attvalue yspace:spacetype -attvalue zspace:spacetype /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc
# input volume is in Talairach space
# thresholding background
[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -short -zero -gt -const 1 /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc
Processing:..............................................Done
# using average brain mask to remove background
Resampling /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc

[nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/resample_labels -clobber -verbose -resample '-like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc' /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /usr/tmp/nu_estimate_np_and_em_10558/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp
[resample_labels] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincresample /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /usr/tmp/resample_labels_10573/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -trilinear -byte  -like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc
Transforming slices:..............................................Done
[resample_labels] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/extracttag /usr/tmp/resample_labels_10573/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -volume /usr/tmp/nu_estimate_np_and_em_10558/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp -threshold 0.5 1.1 -label 1 -maxtags 0
Updating history
(from miopen): Can't write compressed file
ncredef: ncid -1: NetCDF: Not a valid ID
ncattput: ncid -1: NetCDF: Not a valid ID
ncclose: ncid -1: NetCDF: Not a valid ID
resample_labels: crashed while running minc_modify_header (termination status=768)
nu_estimate_np_and_em: crashed while running resample_labels (termination status=768)
--------------------------------------------------------
Test #8 suffered a fatal error.
Consult the file N3/testing/test.log for details and compare with
N3/testing/test_ref.log, a log from a sucessful run of the test suite.

Any help is appreciated.

Thanks!


Harini Eavani
Research Data Analyst
Center for Autism Research
Children's Hospital of Philadelphia
3535 Market Street, Suite 860
Philadelphia, PA 19104