Hello,
I am encountering an error when using mesh2voxel and I cannot pin down exactly what is going on.
This is the error:
mesh2voxel: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access
It does not seem to occur on any other mrtrix function as I am able to successfully execute several others before this stops.
As far as I can tell, the memory on my machine is not full.
When I run it with debug this is what I get:
mesh2voxel: [WARNING] existing output files will be overwritten
mesh2voxel: [DEBUG] No config file found at "/etc/mrtrix.conf"
mesh2voxel: [DEBUG] No config file found at "/home/emma.garrison/.mrtrix.conf"
mesh2voxel: [INFO] opening image "/home/emma.garrison/temp/T1.nii"...
mesh2voxel: [DEBUG] memory-mapping file "/home/emma.garrison/temp/T1.nii"...
mesh2voxel: [DEBUG] file "/home/emma.garrison/temp/T1.nii" mapped at 0x7f1845e84000, size 21627232 (read-only)
mesh2voxel: [DEBUG] transforms_match: FOV difference in scanner coordinates: 0.087246138842508661
mesh2voxel: [DEBUG] unmapping file "/home/emma.garrison/temp/T1.nii"
mesh2voxel: [DEBUG] sanitising image information...
mesh2voxel: [INFO] Axes and transform of image "/home/emma.garrison/temp/T1.nii" altered to approximate RAS coordinate system
mesh2voxel: [DEBUG] searching for suitable phase encoding data...
mesh2voxel: [INFO] image "/home/emma.garrison/temp/T1.nii" opened with dimensions 176x240x256x1, voxel spacing 1.200000047683 7158x1.0546900033950806x1.0546900033950806x0, datatype UInt16BE
mesh2voxel: [INFO] creating image "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif"...
mesh2voxel: [DEBUG] sanitising image information...
mesh2voxel: [DEBUG] creating empty file "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif"
mesh2voxel: [INFO] file "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" already exists - removing
mesh2voxel: [DEBUG] resizing file "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" to 43254372
mesh2voxel: [DEBUG] sanitising image information...
mesh2voxel: [INFO] image "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" created with dimensions 176x240x256x1, voxel spacin g 1.2000000476837158x1.0546900033950806x1.0546900033950806x0, datatype Float32LE
mesh2voxel: [DEBUG] memory-mapping file "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif"...
mesh2voxel: [DEBUG] "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" appears to reside on a networked filesystem - using dela yed write-back
mesh2voxel: [DEBUG] file "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" held in RAM at 0x7f1844800010, size 43253760
mesh2voxel: [DEBUG] image "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" loaded
mesh2voxel: [DEBUG] image "/home/emma.garrison/temp/mesh2voxel_L_Accu.mif" initialised with strides = [ -1 176 42240 10813440 ], start = 175, using direct IO
mesh2voxel: [ 25%] Performing voxel-based segmentation of surface...
mesh2voxel: [DEBUG] sanitising image information...
mesh2voxel: [DEBUG] allocating scratch buffer for image "scratch image"...
mesh2voxel: [DEBUG] image "scratch image" loaded
mesh2voxel: [DEBUG] image "scratch image" initialised with strides = [ -1 176 42240 10813440 ], start = 175, using direct IO
mesh2voxel: [ 38%] Performing voxel-based segmentation of surface...
mesh2voxel: [DEBUG] sanitising image information...
mesh2voxel: [DEBUG] allocating scratch buffer for image "Sum of distances from polygon planes"...
mesh2voxel: [DEBUG] image "Sum of distances from polygon planes" loaded
mesh2voxel: [DEBUG] image "Sum of distances from polygon planes" initialised with strides = [ -1 176 42240 10813440 ], start = 175, using direct IO
mesh2voxel: [ 88%] Performing voxel-based segmentation of surface...
mesh2voxel: [DEBUG] deleting scratch buffer for image "Sum of distances from polygon planes"...
mesh2voxel: [DEBUG] image "Sum of distances from polygon planes" unloaded
mesh2voxel: [DEBUG] deleting scratch buffer for image "scratch image"...
mesh2voxel: [DEBUG] image "scratch image" unloaded
mesh2voxel: [100%] Performing voxel-based segmentation of surface
mesh2voxel: [DEBUG] initialising threads...
mesh2voxel: [DEBUG] launching thread "source"...
mesh2voxel: [DEBUG] launching 24 threads "pipe"...
mesh2voxel: [DEBUG] launching thread "sink"...
mesh2voxel: [DEBUG] waiting for completion of thread "source"...
mesh2voxel: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access
The fault remains even when I turn off multithreading.