[MINC-users] [minctracc] segfault when using -measure option

[Mishkin Derakhshan]

Hi,
I get a segfault whenever I try to use the -measure option.
Here is the simplest example to reproduce the bug.

$ minctracc -measure out.txt t1p.mnc.gz t1p.mnc.gz -transformation
identity.xfm

I'm using:
$ minctracc -version
The program <minctracc> was built from:
mni_autoreg 0.99.60

Here is some info on the files, but I don't think it has to do with the
files themselves as I've tried 100s. Maybe someone else can confirm.
$ mincinfo t1p.mnc.gz
file: t1p.mnc.gz
image: signed__ short 0 to 4095
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     60            3     -93.0427
    yspace                    256    -0.976562      119.239
    xspace                    192    -0.976562      91.5716

$ cat identity.xfm
MNI Transform File
%Sun Sep 25 03:59:15 2016>>> param2xfm -scale 1 1 1 identity.xfm
%(mni_autoreg 0.99.60)

Transform_Type = Linear;
Linear_Transform =
 1 0 0 0
 0 1 0 0
 0 0 1 0;

Looking at the print statements in the debug output from minctracc, and
comparing with minctracc/Main/measure_code.c I have a rough idea where the
segfault must be happening, but it's a little outside my depth at this
point.

Bug happens somewhere in here:
                            /* do var_ratio */

    main_args.obj_function = vr_objective;
    obj_func_val = measure_fit( data, model, mask_data, mask_model,
&main_args );
    (void)fprintf (ofd, "%f - var_ratio\n",obj_func_val);
    (void)fflush(ofd);
    DEBUG_PRINT1 ( "%f - var_ratio\n",obj_func_val);

    delete_volume(data);
    delete_volume(model);

                                /* do ssc / zero-crossings */

    status = input_volume( main_args.filenames.data, 3, default_dim_names,
                          NC_UNSPECIFIED, FALSE, 0.0, 0.0,
                          TRUE, &data, (minc_input_options *)NULL );
    status = input_volume( main_args.filenames.model, 3, default_dim_names,
                          NC_UNSPECIFIED, FALSE, 0.0, 0.0,
                          TRUE, &model, (minc_input_options *)NULL );

    main_args.obj_function = ssc_objective;
    obj_func_val = measure_fit( data, model, mask_data, mask_model,
&main_args );
    (void)fprintf (ofd, "%f - ssc\n",obj_func_val);
    (void)fflush(ofd);
    DEBUG_PRINT1 ( "%f - ssc\n",obj_func_val);


The good news is that the out.txt measure file still gets output, albeit
incomplete, but so does a large core file. Not to mention I can't sleep at
night having a seg fault that is built into the pipeline, er, at least one
that that I know about!

any help?
mishkin

Here is the debugging output from minctracc if that helps:

$ minctracc -measure out.txt t1p.mnc.gz t1p.mnc.gz -transformation
identity.xfm -debug
===== Debugging information from minctracc =====
Data filename       = t1p.mnc.gz
Model filename      = t1p.mnc.gz
Data mask filename  =
Model mask filename =
Input xform name    = identity.xfm
Measure filename    = out.txt

Step size           = 4.000000 4.000000 4.000000
Sub-lattice dia     = 24.000000 24.000000 24.000000
Objective function  = cross correlation (threshold = 0.000000 0.000000)
Transform linear    = TRUE
Transform inverted? = FALSE
Transform type      = 4
Transform matrix    =    1.0000    0.0000    0.0000    0.0000
                         0.0000    1.0000    0.0000    0.0000
                         0.0000    0.0000    1.0000    0.0000
Transform center   =    0.000    0.000    0.000
Transform rotation   =    0.000    0.000    0.000

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Source volume size:  60  by 256  by 192
Source voxel size =    3.000   -0.977   -0.977
Source min/max real range =    0.000 2083.000
Source min/max voxel=    0.000 2083.000

Target volume size:  60  by 256  by 192
Target voxel =    3.000   -0.977   -0.977
Target min/max real range=    0.000 2083.000
Target min/max voxel =    0.000 2083.000


  using input transformation to get initial parameters:
   Center of rot/scale not forced, will be set to : 0.000000 0.000000
0.000000
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
slice lim 0 44
row lim   1 62
col lim   1 46
thresh =    0.00000    0.00000
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
Source volume is smallest
Lattice step size  =   -4.000   -4.000    4.000
Lattice start      =   88.104  129.917  -72.203
Lattice count      =       46       62       45

 128340  128340  128340 ->        inf
inf - zscore
 128340  128340 -> 0.00000000
0.000000 - xcorr
 128340  128340       0 -> 0.20877945
0.208779 - var_ratio
Segmentation fault