[MINC-users] minc file is not visible in register but is visible in Display
Robert D. Vincent
bert at phalarope.com
Thu May 18 18:47:25 EDT 2017
Hi,
Sorry, I replied to this earlier but used the wrong email address, so that
message is probably awaiting moderation.
A more recent version of Register might help. Some versions can't deal with
float volumes in the range 0-1. Anything built off the current develop
branch should be fine.
I'm not certain it will help with your version, but it might be useful to
try this:
register -global Volume_voxel_type 0 subject_t2map.mnc.gz
-bert
On Thu, May 18, 2017 at 6:37 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> 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
> >
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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