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

Thu May 18 18:37:48 EDT 2017

Bert can probably be more specific, but there is a (more recent?) version
of register that does the right thing on volumes like this.

On Thu, May 18, 2017 at 4:02 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> It's a bug in certain versions of register, affecting it's ability to show
> files stored in float, with low values.
> Can be fixed by mincreshape -short
>
>
>
> On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote:
>
>> 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?
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>