/var/drc/scratch1/malone/nipype_deps_2017_01_17/bin/reg_average --cmd_file /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/ave_ims_b0/reg_average_cmd

reg_average /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/ave_ims_b0/avg_out.nii.gz -avg /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0000.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0017.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0033.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0049.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0068.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0085.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0101.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0117.nii.gz /var/drc/research/emilyphd/yoad/modified_pipeline_jan2017A/01-003/dmri_workflow/split_dwis/dwi_0136.nii.gz

[NiftyReg WARNING] Function: reg_io_checkFileFormat
[NiftyReg WARNING] No filename extension provided - the Nifti library is used by default
** ERROR (nifti_image_read): failed to find header file for ''
Segmentation fault (core dumped)

       avg_output_image = reg_io_ReadImageFile(referenceImageName);

index e0802d1..3c87881 100644
--- a/reg-lib/cpu/_reg_maths_eigen.cpp
+++ b/reg-lib/cpu/_reg_maths_eigen.cpp
@@ -282,6 +282,7 @@ void reg_mat33_logm(mat33 *in_tensor)
 
    // Convert to Eigen format
    bool all_zeros = true;
+   double det = 0;
    for (sm = 0; sm < 3; sm++){
       for (sn = 0; sn < 3; sn++){
          float val=in_tensor->m[sm][sn];
@@ -290,7 +291,14 @@ void reg_mat33_logm(mat33 *in_tensor)
          tensor(sm, sn) = static_cast<double>(val);
       }
    }
-   if(all_zeros==true){
+   // Actually R case requires invertible and no negative real ev,
+   // but the only observed case so far was non-invertible.
+   // determinant is not a perfect check for invertibility and
+   // identity with zero not great either, but the alternative
+   // is a general eigensolver and the logarithm function should
+   // succeed unless convergence just isn't happening.
+   det = tensor.determinant();
+   if(all_zeros==true || det == 0){
       reg_mat33_to_nan(in_tensor);
       return;
    }

[valette@desk reg-apps]$ ls ~/volumes
vol1.nii.gz  vol2.nii.gz  vol3.nii.gz

[valette@desk reg-apps]$ more params.sh 
#!/bin/sh

############################################################################
###################### PARAMETERS THAT CAN BE CHANGED ######################
############################################################################
# Array that contains the input images to create the atlas
export IMG_INPUT=(`ls ~/volumes/*.nii.gz`)
export IMG_INPUT_MASK= # leave empty to not use floating masks

# template image to use to initialise the atlas creation
export TEMPLATE=`echo ~/volumes/vol1.nii.gz`
export TEMPLATE_MASK= # leave empty to not use a reference mask

# folder where the result images will be saved
export RES_FOLDER=`pwd`/groupwise_result

# argument to use for the affine (reg_aladin)
export AFFINE_args="-omp 4"
# argument to use for the non-rigid registration (reg_f3d)
export NRR_args="-omp 4"

# number of affine loop to perform - Note that the first step is always rigid
export AFF_IT_NUM=5
# number of non-rigid loop to perform
export NRR_IT_NUM=10

# grid engine arguments
export QSUB_CMD="qsub -l h_rt=05:00:00 -l tmem=0.9G -l h_vmem=0.9G -l vf=0.9G -l s_stack=10240  -j y -S /bin/csh -b y -cwd -V -R y -pe smp 4"
############################################################################

[valette@desk reg-apps]$ sh ./groupwise_niftyreg_run.sh ./params.sh 

************************************************************
>>> There are 3 input images to groupwise register <<<
>>> The template image to initialise the registration is /home/valette/volumes/vol1.nii.gz <<<
************************************************************

The output image folder (/home/valette/git/niftyreg/reg-apps/groupwise_result) does not exist
The output image folder (/home/valette/git/niftyreg/reg-apps/groupwise_result) has been created
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/dev/null.nii'
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/dev/null.nii'
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/dev/null.nii'
[NiftyReg WARNING] Function: reg_io_checkFileFormat
[NiftyReg WARNING] No filename extension provided - the Nifti library is used by default
** ERROR (nifti_image_read): failed to find header file for '/home/valette/git/niftyreg/reg-apps/groupwise_result/aff_1/aff_mat_vol1_it1.txt'
./groupwise_niftyreg_run.sh : ligne 309 : 28166 Segmentation fault      (core dumped)reg_average ${RES_FOLDER}/aff_${CUR_IT}/average_affine_it_${CUR_IT}.nii.gz -demean1 ${averageImage} ${list_average}
Error when creating 						/home/valette/git/niftyreg/reg-apps/groupwise_result/aff_1/average_affine_it_1.nii.gz

/usr/local/cuda-9.0/include/crt/host_config.h:119:2: error: #error -- unsupported GNU version! gcc versions later than 6 are not supported!
 #error -- unsupported GNU version! gcc versions later than 6 are not supported!

 CMAKE_CXX_COMPILER               /usr/bin/c++                                                                                                         
 CMAKE_CXX_COMPILER_AR            /usr/bin/gcc-ar-7                                                                                                    
 CMAKE_CXX_COMPILER_RANLIB        /usr/bin/gcc-ranlib-7                                                                                                                                                                                           
 CMAKE_C_COMPILER                 /usr/bin/cc                                                                                                          
 CMAKE_C_COMPILER_AR              /usr/bin/gcc-ar-7                                                                                                    
 CMAKE_C_COMPILER_RANLIB          /usr/bin/gcc-ranlib-7     

 …/niftyreg/build   master ?  make                                                                                         ✔  13:24 Dur  12:12:48
Scanning dependencies of target z
[  1%] Building C object reg-io/zlib/CMakeFiles/z.dir/adler32.c.o
[  2%] Building C object reg-io/zlib/CMakeFiles/z.dir/compress.c.o
[  3%] Building C object reg-io/zlib/CMakeFiles/z.dir/crc32.c.o
[  4%] Building C object reg-io/zlib/CMakeFiles/z.dir/gzio.c.o
[  5%] Building C object reg-io/zlib/CMakeFiles/z.dir/uncompr.c.o
[  5%] Building C object reg-io/zlib/CMakeFiles/z.dir/deflate.c.o
[  6%] Building C object reg-io/zlib/CMakeFiles/z.dir/trees.c.o
[  7%] Building C object reg-io/zlib/CMakeFiles/z.dir/zutil.c.o
[  8%] Building C object reg-io/zlib/CMakeFiles/z.dir/inflate.c.o
[  9%] Building C object reg-io/zlib/CMakeFiles/z.dir/infback.c.o
[ 10%] Building C object reg-io/zlib/CMakeFiles/z.dir/inftrees.c.o
[ 11%] Building C object reg-io/zlib/CMakeFiles/z.dir/inffast.c.o
[ 12%] Linking C static library libz.a
[ 12%] Built target z
Scanning dependencies of target png
[ 13%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/png.c.o
[ 14%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngerror.c.o
[ 15%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngget.c.o
[ 16%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngmem.c.o
[ 17%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngpread.c.o
[ 18%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngread.c.o
[ 19%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngrio.c.o
[ 19%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngrtran.c.o
[ 20%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngrutil.c.o
[ 21%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngset.c.o
[ 22%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngtrans.c.o
[ 23%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngwio.c.o
[ 24%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngwrite.c.o
[ 25%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngwtran.c.o
[ 25%] Building C object reg-io/png/CMakeFiles/png.dir/lpng1510/pngwutil.c.o
[ 26%] Linking C static library libpng.a
[ 26%] Built target png
Scanning dependencies of target _reg_maths
[ 27%] Building CXX object reg-lib/CMakeFiles/_reg_maths.dir/cpu/_reg_maths.cpp.o
[ 28%] Building CXX object reg-lib/CMakeFiles/_reg_maths.dir/cpu/_reg_maths_eigen.cpp.o
[ 29%] Linking CXX static library lib_reg_maths.a
[ 29%] Built target _reg_maths
Scanning dependencies of target reg_nifti
[ 30%] Building C object reg-io/nifti/CMakeFiles/reg_nifti.dir/nifti1_io.c.o
[ 31%] Building C object reg-io/nifti/CMakeFiles/reg_nifti.dir/znzlib.c.o
[ 31%] Linking C static library libreg_nifti.a
[ 31%] Built target reg_nifti
Scanning dependencies of target _reg_tools
[ 32%] Building CXX object reg-lib/CMakeFiles/_reg_tools.dir/cpu/_reg_tools.cpp.o
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp: In instantiation of ‘void reg_intensityRescale_core(nifti_image*, int, float, float) [with DTYPE = unsigned char]’:
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp:203:80:   required from here
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp:133:17: warning: large integer implicitly truncated to unsigned type [-Woverflow]
       currentMax=-(DTYPE)std::numeric_limits<short>::max();
       ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp:141:17: warning: large integer implicitly truncated to unsigned type [-Woverflow]
       currentMax=-(DTYPE)std::numeric_limits<int>::max();
       ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp: In instantiation of ‘void reg_intensityRescale_core(nifti_image*, int, float, float) [with DTYPE = short unsigned int]’:
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp:209:81:   required from here
/home/fernando/git/niftyreg/reg-lib/cpu/_reg_tools.cpp:141:17: warning: large integer implicitly truncated to unsigned type [-Woverflow]
[ 32%] Linking CXX static library lib_reg_tools.a
[ 32%] Built target _reg_tools
Scanning dependencies of target reg_png
[ 33%] Building CXX object reg-io/png/CMakeFiles/reg_png.dir/reg_png.cpp.o
[ 34%] Building CXX object reg-io/png/CMakeFiles/reg_png.dir/readpng.cpp.o
[ 35%] Linking CXX static library libreg_png.a
[ 35%] Built target reg_png
Scanning dependencies of target _reg_ReadWriteImage
[ 35%] Building CXX object reg-io/CMakeFiles/_reg_ReadWriteImage.dir/_reg_ReadWriteImage.cpp.o
[ 36%] Building CXX object reg-io/CMakeFiles/_reg_ReadWriteImage.dir/_reg_ReadWriteMatrix.cpp.o
[ 37%] Building CXX object reg-io/CMakeFiles/_reg_ReadWriteImage.dir/_reg_ReadWriteBinary.cpp.o
/home/fernando/git/niftyreg/reg-io/_reg_ReadWriteBinary.cpp: In function ‘void readFloatBinaryArray(const char*, int, float*)’:
/home/fernando/git/niftyreg/reg-io/_reg_ReadWriteBinary.cpp:8:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         fread((void*)(&currentValue), sizeof(currentValue), 1, infile);
         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/fernando/git/niftyreg/reg-io/_reg_ReadWriteBinary.cpp: In function ‘void readIntBinaryArray(const char*, int, int*)’:
/home/fernando/git/niftyreg/reg-io/_reg_ReadWriteBinary.cpp:18:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         fread((void*)(&currentValue), sizeof(currentValue), 1, infile);
         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 38%] Building CXX object reg-io/CMakeFiles/_reg_ReadWriteImage.dir/_reg_stringFormat.cpp.o
[ 39%] Linking CXX static library lib_reg_ReadWriteImage.a
[ 39%] Built target _reg_ReadWriteImage
[ 40%] Building NVCC (Device) object reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/_reg_common_cuda_generated__reg_common_cuda.cu.o
In file included from /usr/local/cuda-9.0/include/host_config.h:50:0,
                 from /usr/local/cuda-9.0/include/cuda_runtime.h:78,
                 from <command-line>:0:
/usr/local/cuda-9.0/include/crt/host_config.h:119:2: error: #error -- unsupported GNU version! gcc versions later than 6 are not supported!
 #error -- unsupported GNU version! gcc versions later than 6 are not supported!
  ^~~~~
CMake Error at _reg_common_cuda_generated__reg_common_cuda.cu.o.Release.cmake:219 (message):
  Error generating
  /home/fernando/git/niftyreg/build/reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir//./_reg_common_cuda_generated__reg_common_cuda.cu.o


reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/build.make:63: recipe for target 'reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/_reg_common_cuda_generated__reg_common_cuda.cu.o' failed
make[2]: *** [reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/_reg_common_cuda_generated__reg_common_cuda.cu.o] Error 1
CMakeFiles/Makefile2:876: recipe for target 'reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/all' failed
make[1]: *** [reg-lib/cuda/CMakeFiles/_reg_common_cuda.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

Copyright (c) 2009, University College London. All rights reserved.

Copyright (c) 2009-2018, University College London
Copyright (c) 2018, NiftyReg Developers.
All rights reserved.

Copyright (c) 2009, University College London, United-Kingdom
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

Neither the name of the University College London nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.

diff --git a/reg-apps/reg_f3d.cpp b/reg-apps/reg_f3d.cpp
index 42e9f59..787ff2e 100755
--- a/reg-apps/reg_f3d.cpp
+++ b/reg-apps/reg_f3d.cpp
@@ -173,7 +173,7 @@ int main(int argc, char **argv)
    omp_set_num_threads(defaultOpenMPValue);
 #endif
 
-   char text[1024];
+   char *text=0, *tmptext;
    //\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
    // Check if any information is required
    for(int i=1; i<argc; i++)
@@ -218,11 +218,21 @@ int main(int argc, char **argv)
 #endif
       reg_print_info((argv[0]), "");
       reg_print_info((argv[0]), "Command line:");
-      sprintf(text, "\t");
-      for(int i=0; i<argc; i++)
-         sprintf(text+strlen(text), " %s", argv[i]);
+      if (asprintf(&text, "\t") < 0) {
+       reg_print_info((argv[0]), "Out of memory storing command line");
+       return EXIT_FAILURE;
+      }
+      for(int i=0; i<argc; i++) {
+       if (asprintf(&tmptext, "%s %s", text, argv[i]) < 0) {
+         reg_print_info((argv[0]), "Out of memory storing command line");
+         return EXIT_FAILURE;
+       }
+       free(text);
+       text=tmptext;
+      }
       reg_print_info((argv[0]), text);
       reg_print_info((argv[0]), "");
+      free(text); text=0;
 #ifdef NDEBUG
    }
 #endif
@@ -730,8 +740,9 @@ int main(int argc, char **argv)
    if(verbose)
    {
       int maxThreadNumber = omp_get_max_threads();
-      sprintf(text, "OpenMP is used with %i thread(s)", maxThreadNumber);
+      asprintf(&text, "OpenMP is used with %i thread(s)", maxThreadNumber);
       reg_print_info((argv[0]), text);
+      free(text); text=0;
    }
 #endif // _OPENMP
 
@@ -843,9 +854,10 @@ int main(int argc, char **argv)
       time(&end);
       int minutes=(int)floorf((end-start)/60.0f);
       int seconds=(int)(end-start - 60*minutes);
-      sprintf(text, "Registration performed in %i min %i sec", minutes, seconds);
+      asprintf(&text, "Registration performed in %i min %i sec", minutes, seconds);
       reg_print_info((argv[0]), text);
       reg_print_info((argv[0]), "Have a good day !");
+      free(text); text=0;
 #ifdef NDEBUG
    }
 #endif

#include <stdlib.h>
#include <stdio.h>
#include <stdarg.h>

#ifndef _GNU_SOURCE

int vasprintf(char **strp, const char *fmt, va_list ap) {
  va_list ap2;
  va_copy(ap2, ap);
  int str_len, need_len;
  str_len = vsnprintf(0, 0, fmt, ap);
  need_len = str_len + 1;
  *strp = malloc(need_len);
  if (*strp) {
    vsnprintf(*strp, need_len, fmt, ap2);
  } else {
    *strp = 0;
    str_len = -1;
  }
  va_end(ap2);
  return str_len;
}

int asprintf(char **strp, const char *fmt, ...) {
  va_list ap;
  va_start(ap, fmt);
  int ret_val = vasprintf(strp, fmt, ap);
  va_end(ap);
  return ret_val;
}

#endif