fixelcfestats: abnormal termination when doing t-tests + f-test #2289
Description
Describe the bug
I am trying to run the fixelcfestats to perform hypothesis testing for multiple contrasts + an f-test, but the process terminates abruptly while calculating the basic properties of the default permutation, even when I use the -notest flag:
fixelcfestats -force smoothed_fixel_data list_of_files.txt design_matrix.txt contrasts.txt wm_fixel_connectivity stats_results -mask fixel_mask.mif -exchange_within blocks.txt -variance blocks.txt -ftests ftests.txt -notest
fixelcfestats: [WARNING] existing output files will be overwritten
fixelcfestats: Number of fixels in template: 574477
fixelcfestats: Number of fixels in mask: 498510
fixelcfestats: [done] Configuring data import from files listed in "list_of_files.txt" as found relative to directory "smoothed_fixel_data"
fixelcfestats: Number of inputs: 8
fixelcfestats: Number of factors: 6
fixelcfestats: Design matrix condition number: 14.3611
fixelcfestats: Number of variance groups: 2
fixelcfestats: Number of hypotheses: 5
fixelcfestats: [WARNING] A total of 15032 fixels in the provided mask do not possess any streamlines-based connectivity; these will not be enhanced by CFE, and hence cannot be tested for statistical significance
fixelcfestats: [100%] Loading fixel data (no smoothing)
fixelcfestats: [ 6%] Calculating basic properties of default permutation...double free or corruption (out)
Aborted (core dumped)
It should be mentioned I am including two different measures in the testing so I have 2 exchangeability blocks and variance blocks while the design matrix also has 2 blocks, however It works without problem when:
- I add the
-fonlyflag -> Only F-test - I don't add the
-ftestsoption -> Only t-tests
To Reproduce
Data I used to reproduce the error: https://drive.google.com/file/d/1U3rIOQ9T8DvVXH3wCNycKuohx4pM_VLD/view?usp=sharing
Platform/Environment/Version
-
OS: Ubuntu 18.04.4 LTS
-
MRtrix3 version: 3.0.2-246-g861c004f
Advanced debugging information
This is what happens when debugging:
diana@expe:/mnt/md0/min_example_ftests_contrasts$ gdb --args fixelcfestats -force smoothed_fixel_data list_of_files.txt design_matrix.txt contrasts.txt wm_fixel_connectivity stats_results -mask fixel_mask.mif -exchange_within blocks.txt -variance blocks.txt -ftests ftests.txt -notest
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Reading symbols from fixelcfestats...(no debugging symbols found)...done.
(gdb) r
Starting program: /mnt/md0/mrtrix3/bin/fixelcfestats -force smoothed_fixel_data list_of_files.txt design_matrix.txt contrasts.txt wm_fixel_connectivity stats_results -mask fixel_mask.mif -exchange_within blocks.txt -variance blocks.txt -ftests ftests.txt -notest
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
fixelcfestats: [WARNING] existing output files will be overwritten
fixelcfestats: Number of fixels in template: 574477
fixelcfestats: Number of fixels in mask: 498510
fixelcfestats: [done] Configuring data import from files listed in "list_of_files.txt" as found relative to directory "smoothed_fixel_data"
fixelcfestats: Number of inputs: 8
fixelcfestats: Number of factors: 6
fixelcfestats: Design matrix condition number: 14.3611
fixelcfestats: Number of variance groups: 2
fixelcfestats: Number of hypotheses: 5
fixelcfestats: [WARNING] A total of 15032 fixels in the provided mask do not possess any streamlines-based connectivity; these will not be enhanced by CFE, and hence cannot be tested for statistical significance
fixelcfestats: [100%] Loading fixel data (no smoothing)
[New Thread 0x7ffe594f3700 (LWP 31227)]
fixelcfestats: [ 0%] Calculating basic properties of default permutation...[New Thread 0x7ffe58cf2700 (LWP 31228)]
fixelcfestats: [ 2%] Calculating basic properties of default permutation...[New Thread 0x7ffe53fff700 (LWP 31229)]
fixelcfestats: [ 3%] Calculating basic properties of default permutation...[New Thread 0x7ffe537fe700 (LWP 31230)]
[New Thread 0x7ffe52ffd700 (LWP 31231)]
[New Thread 0x7ffe527fc700 (LWP 31232)]
fixelcfestats: [ 4%] Calculating basic properties of default permutation...[New Thread 0x7ffe51ffb700 (LWP 31233)]
[New Thread 0x7ffe517fa700 (LWP 31234)]
fixelcfestats: [ 5%] Calculating basic properties of default permutation...[New Thread 0x7ffe50ff9700 (LWP 31235)]
[New Thread 0x7ffe33fff700 (LWP 31236)]
double free or corruption (out)
fixelcfestats: [ 7%] Calculating basic properties of default permutation...
Thread 9 "fixelcfestats" received signal SIGABRT, Aborted.
[Switching to Thread 0x7ffe517fa700 (LWP 31234)]
__GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51
51 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51
#1 0x00007ffff6a078b1 in __GI_abort () at abort.c:79
#2 0x00007ffff6a50907 in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff6b7ddfa "%s\n") at ../sysdeps/posix/libc_fatal.c:181
#3 0x00007ffff6a5797a in malloc_printerr (str=str@entry=0x7ffff6b7fad0 "double free or corruption (out)") at malloc.c:5350
#4 0x00007ffff6a5eee5 in _int_free (have_lock=0, p=0x7ffe38000d90, av=0x7ffff6db2c40 <main_arena>) at malloc.c:4278
#5 __GI___libc_free (mem=0x7ffe38000da0) at malloc.c:3124
#6 0x00007ffff7b49507 in MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&) ()
from /mnt/md0/mrtrix3/bin/../lib/libmrtrix.so
#7 0x00007ffff7b4b399 in MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor::operator()(unsigned long const&) () from /mnt/md0/mrtrix3/bin/../lib/libmrtrix.so
#8 0x00007ffff7b4b499 in MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >::execute() () from /mnt/md0/mrtrix3/bin/../lib/libmrtrix.so
#9 0x00007ffff7b2f57d in std::_Function_handler<std::unique_ptr<std::__future_base::_Result_base, std::__future_base::_Result_base::_Deleter> (), std::__future_base::_Task_setter<std::unique_ptr<std::__future_base::_Result<void>, std::__future_base::_Result_base::_Deleter>, std::thread::_Invoker<std::tuple<void (MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >::*)(), MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >*> >, void> >::_M_invoke(std::_Any_data const&) () from /mnt/md0/mrtrix3/bin/../lib/libmrtrix.so
#10 0x0000555555572c79 in std::__future_base::_State_baseV2::_M_do_set(std::function<std::unique_ptr<std::__future_base::_Result_base, std::__future_base::_Result_base::_Deleter> ()>*, bool*) ()
#11 0x00007ffff6dc7827 in __pthread_once_slow (once_control=0x5555558b07f8, init_routine=0x7ffff76498a0 <__once_proxy>) at pthread_once.c:116
#12 0x00007ffff7b35c3f in std::thread::_State_impl<std::thread::_Invoker<std::tuple<std::__future_base::_Async_state_impl<std::thread::_Invoker<std::tuple<void (MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >::*)(), MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >*> >, void>::_Async_state_impl(std::thread::_Invoker<std::tuple<void (MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >::*)(), MR::Thread::(anonymous namespace)::__Sink<MR::Thread::(anonymous namespace)::__Batch<unsigned long>, MR::Thread::(anonymous namespace)::__Multi<MR::Math::Stats::GLM::all_stats(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, MR::vector<MR::Math::Stats::CohortDataImport, 0> const&, MR::vector<MR::Math::Stats::GLM::Hypothesis, 0> const&, Eigen::Array<unsigned long, -1, 1, 0, -1, 1> const&, Eigen::Array<double, -1, 1, 0, -1, 1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1>&)::Functor> >*> >&&)::{lambda()#1}> > >::_M_run() () from /mnt/md0/mrtrix3/bin/../lib/libmrtrix.so
#13 0x00007ffff764a6df in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
---Type <return> to continue, or q <return> to quit---
#14 0x00007ffff6dbf6db in start_thread (arg=0x7ffe517fa700) at pthread_create.c:463
#15 0x00007ffff6ae8a3f in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95