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BIC-MNI / minc-tools

Basic minc-tools from former minc repository
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volume_stats: Assertion failed in CachedArray.cc AND seg fault in spline_smooth #101

Closed eds-slim closed 4 years ago

eds-slim commented 4 years ago

Hello, in the context of pre-processing some rs-fMRI data I am running freesurfer on an HPC. However, I am receiving segmentation faults in mri_convert which I have been able to track to a problem with volume_stats and smooth_spline:

From the mri folder of my subject's freesurfer tree I run

/opt/freesurfer/mni/bin/volume_stats -all ./tmp.mri_nu_correct.mni.15919/0/nu0__.mnc -debug -verbose

which results in

Reading volume /work/test2/01387fs/mri/tmp.mri_nu_correct.mni.15919/0/nu0__.mncDone
C1:32609792:32768 C2:31554272:32768
Created blocks:
  32609792
  31554272
Assertion failed at line 742 in file templates/CachedArray.cc

Line 742 reads assert(_s.is_open());

Interestingly, when I run volume_stats with the -noache flag, the error disappears, namely

Reading volume /work/test2/01387fs/mri/tmp.mri_nu_correct.mni.15919/0/nu0__.mncDone
Scanning ./tmp.mri_nu_correct.mni.15919/0/nu0__.mnc.................................................................Done
Creating histogram with 256 bins, bin width 1...Done
File:         ./tmp.mri_nu_correct.mni.15919/0/nu0__.mnc
# voxels:     274625
% of total:   100
Volume (mm3): 1.7576e+07
Min:          0
Max:          255
Sum:          7.07616e+06
Sum2:         8.35459e+08
Mean:         25.7666
Variance:     2378.26
Stddev:       48.7674
Median:       2
Majority:     0
BiModalT:     59
PctT (-1.79769e+308):    -0.5 255.5
Entropy:      4.42151
CoM_voxel:    xspace:31.9172 yspace:35.3371 zspace:29.0955
CoM_world:    zspace:-47.3955 yspace:-16.2662 xspace:-3.46566

In https://github.com/BIC-MNI/N3/blob/master/src/VolumeStats/volumeStats.cc, the only difference caused by the -nocache flag appears to be the use of CachedArray instead of SimpleArray. To test the functionality of CachedArray I compiled test.cc from https://github.com/BIC-MNI/EBTKS/tree/master/src which runs on my cluster without error.

When I patch freesurfer so as to use the -nocache option in volume_stats as explained on https://mailman.bic.mni.mcgill.ca/pipermail/minc-users/2008-April/001996.html, the program exits at

/opt/freesurfer/mni/bin/spline_smooth -clobber -verbose -full_support -distance 50 -b_spline -lambda 1.0e-7 -subsample 1 -mask ./tmp.mri_nu_correct.mni.27342/0/nu1_mask.mnc ./tmp.mri_nu_correct.mni.27342/0/nu1_temp.mnc ./tmp.mri_nu_correct.mni.27342/0/nu1_residue.mnc
nu_estimate_np_and_em: crashed while running spline_smooth (termination status=11)

Repeating the latest command gives a simple Segmentation Fault without further information.

So there is 1) A problem related to CachedArray and asserting the successful opening of a temporary file 2) a seg fault in spline_smooth which I am unable to track down further.

All commands can be run successfully with the same input files on my local computer. One of the hardware peculiarities on the cluster I am aware of is the inability to create hard links. Soft links are permitted.

This problem appears to have popped up now and again in various mailing lists, but so far no definitive solution has transpired. Thanks!

vfonov commented 4 years ago

I suggest trying with recent version of minc-toolkit (i.e 1.9.17) , freesurfer still bundles version of minc of 1.5.1 with tools from around 2007

gdevenyi commented 4 years ago

Please reopen if updated minc-tools still have this issue.