[MINC-users] minc file is not visible in register but is visible in Display

Thu May 18 15:47:29 EDT 2017

Hi,
I have a file that when viewed in register is not viewable at all. It is
just blank (black) everywhere no matter what I do with the windowing.
When I load it in Display it is just fine, so I know the data is there.

It is a systemic problem, i.e., all files that are created with my script
have this problem of not being visible in register.

I'm wondering if it has something to do with the range of my data because
if I do further operations on it, then the downstream files load okay.

For example, the file that currently does not load is subject_t2map.mnc.gz
which contains float values from 0 to 1.

If I do something like this, then the resulting 100.mnc loads just fine in
register:
minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc

Here are the mincstats of my file with/without a mask:

localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz
File:              subject_t2map.mnc.gz
Mask file:         (null)
Total voxels:      3932160
# voxels:          2178980
% of total:        55.41432699
Volume (mm3):      6536940
Min:               0
Max:               0.9998887777
Sum:               415156.0653
Sum^2:             161711.3365
Mean:              0.1905277081
Variance:          0.03791344611
Stddev:            0.1947137543
CoM_voxel(z,y,x):  30.68098471 128.9858818 128.9017075
CoM_real(x,y,z):   2.09258826 70.06459185 43.54402081

Histogram:         (null)
Total voxels:      3932160
# voxels:          2178980
% of total:        55.41432699
Median:            0.1142372932
Majority:          0.0002499721886
BiModalT:          0.3392122686
PctT [  0%]:       0.0002499721886
Entropy :          9.187178001

localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask
subject_t2map_mask.mnc.gz -mask_binvalue 1.0
File:              subject_t2map.mnc.gz
Mask file:         subject_t2map_mask.mnc.gz
Total voxels:      3932160
# voxels:          1962553
% of total:        49.91030375
Volume (mm3):      5887659
Min:               0.01020694431
Max:               0.9998887777
Sum:               415156.0653
Sum^2:             161711.3365
Mean:              0.211538779
Variance:          0.0376498199
Stddev:            0.194035615
CoM_voxel(z,y,x):  30.68098471 128.9858818 128.9017075
CoM_real(x,y,z):   2.09258826 70.06459185 43.54402081

Histogram:         (null)
Total voxels:      3932160
# voxels:          1962553
% of total:        49.91030375
Median:            0.1242361822
Majority:          0.09273968637
BiModalT:          0.3552104831
PctT [  0%]:       0.0002499721886
Entropy :          9.681988728

And here is the full mincheader:
localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz
netcdf mincheader-18621-tmp {
dimensions:
zspace = 60 ;
yspace = 256 ;
xspace = 256 ;
variables:
double zspace(zspace) ;
zspace:varid = "MINC standard variable" ;
zspace:vartype = "dimension____" ;
zspace:version = "MINC Version    1.0" ;
zspace:comments = "Z increases from patient inferior to superior" ;
zspace:spacing = "regular__" ;
zspace:alignment = "centre" ;
zspace:step = 3. ;
zspace:start = -53.5106888535874 ;
zspace:spacetype = "native____" ;
zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855,
0.997490804617524 ;
int yspace ;
yspace:varid = "MINC standard variable" ;
yspace:vartype = "dimension____" ;
yspace:version = "MINC Version    1.0" ;
yspace:comments = "Y increases from patient posterior to anterior" ;
yspace:spacing = "regular__" ;
yspace:alignment = "centre" ;
yspace:step = -1. ;
yspace:start = 201.955416409066 ;
yspace:spacetype = "native____" ;
yspace:direction_cosines = 0.0303997023189596, 0.997088076060185,
0.0699373053349794 ;
int xspace ;
xspace:varid = "MINC standard variable" ;
xspace:vartype = "dimension____" ;
xspace:version = "MINC Version    1.0" ;
xspace:comments = "X increases from patient left to right" ;
xspace:spacing = "regular__" ;
xspace:alignment = "centre" ;
xspace:step = -1. ;
xspace:start = 128.433460913677 ;
xspace:spacetype = "native____" ;
xspace:direction_cosines = 0.999498332440992, -0.0297021098791549,
-0.0109940036566919 ;
double image-max(zspace) ;
image-max:varid = "MINC standard variable" ;
image-max:vartype = "var_attribute" ;
image-max:version = "MINC Version    1.0" ;
image-max:_FillValue = 1. ;
image-max:parent = "image" ;
double image-min(zspace) ;
image-min:varid = "MINC standard variable" ;
image-min:vartype = "var_attribute" ;
image-min:version = "MINC Version    1.0" ;
image-min:_FillValue = 0. ;
image-min:parent = "image" ;
float image(zspace, yspace, xspace) ;
image:parent = "rootvariable" ;
image:varid = "MINC standard variable" ;
image:vartype = "group________" ;
image:version = "MINC Version    1.0" ;
image:image-max = "--->image-max" ;
image:image-min = "--->image-min" ;
image:valid_range = 0.f, 0.9998888f ;
image:complete = "true_" ;
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version    1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "image" ;

// global attributes:
:ident = "redacted" ;
:minc_version = "2.2.00" ;
:history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult
subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n",
"" ;
}

And here is my minc package info stuff:
localhost[~/nrx/t2map]$ which register
/opt/minc-toolkit/0.3.16/bin/register

localhost[~/nrx/t2map]$ register -version
register:  Version: 1.4.00

localhost[~/nrx/t2map]$ mincstats -version
program: 2.2.00
libminc: 2.2.00
netcdf : 4.2.1 of Feb 19 2015 15:50:30 $
HDF5   : 1.8.8

localhost[~/nrx/t2map]$ cat /etc/system-release
CentOS release 6.5 (Final)

localhost[~/nrx/t2map]$ uname -a
Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19
21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Any come across this bug before? Any ideas on how to fix it so it is
viewable in register?