[MINC-users] minc file is not visible in register but is visible in Display
Mishkin Derakhshan
mishkind at gmail.com
Fri May 19 16:22:20 EDT 2017
Bert, I tried that command but it just spits out the usage. I'm guessing my
version of register doesn't have that global. I grepped through the output
of `strings register` and indeed I didn't find any variable named
Volume_voxel_type.
Vlad, mincresahpe as a short worked so that is probably the workaround we
will use instead of getting everyone to install a new version of register
at this point.
thanks,
mishkin
On Thu, May 18, 2017 at 12:47 PM, Robert D. Vincent <bert at phalarope.com>
wrote:
> 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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