[MINC-users] N3 problem (Vladimir Fonov)

[Popescu, V.]

Dear Vladimir,
Thanks for your answer. 
I ran the mincheader command and I got the following output.
It looks fine to me. Plus I converted the image from nifti and not
directly from DICOM. 


netcdf Manbetset143_noneck {
dimensions:
        xspace = 128 ;
        yspace = 240 ;
        zspace = 196 ;
variables:
        int rootvariable ;
                rootvariable:varid = "MINC standard variable" ;
                rootvariable:vartype = "group________" ;
                rootvariable:version = "MINC Version    1.0" ;
                rootvariable:parent = "" ;
                rootvariable:children = "image" ;
        double 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 = 1.20000004768372 ;
                xspace:start = -74.5828010946915 ;
                xspace:direction_cosines = -0.995703348275213,
0.0888212777983069, -0.0261844007723182 ;
                xspace:units = "mm" ;
        double 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 = -105.174504296302 ;
                yspace:direction_cosines = 0.08885174879246,
0.996044861809147, -3.43728227382414e-07 ;
                yspace:units = "mm" ;
        double 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 = 1. ;
                zspace:start = -141.503699403711 ;
                zspace:direction_cosines = -0.0260808070375557,
0.00232687191043303, 0.999657129805706 ;
                zspace:units = "mm" ;
        double image-min ;
                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" ;
        double image-max ;
                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" ;
        float image(xspace, yspace, zspace) ;
                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:complete = "true_" ;
                image:signtype = "signed__" ;
                image:valid_range = 0.f, 1078.f ;

// global attributes:
                :history = "" ;
data:

 rootvariable = _ ;

 xspace = 0 ;

 yspace = 0 ;

 zspace = 0 ;

 image-min = _ ;

 image-max = 1078 ;
}
Today's Topics:

   1. Re: N3 problem (Vladimir Fonov)
   2. mincaverage gives float numbers for integers (Ji Hyum KO)


----------------------------------------------------------------------

Message: 1
Date: Wed, 15 Sep 2010 15:09:04 -0400
From: Vladimir Fonov <vladimir.fonov at gmail.com>
Subject: Re: [MINC-users] N3 problem
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
	<AANLkTimLVqRUe5Y8K525uhOK4HW4=Att9jmcP2BDAV_E at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello,


sometimes this kind of a problem is caused by irregular sampling of
the minc file (it usually happens due to the glitches in dicom to minc
conversion). You can check if it is the case by using mincheader
command and searching for irregular word in image dimensions
description part ( xspace,yspace,zspace attributes)

On Wed, Sep 15, 2010 at 11:32 AM, Popescu, V. <v.popescu at vumc.nl> wrote:
> Dear all,
> I have a problem running standard N3. It works perfectly on all scans
> except for one, and I cannot see any striking difference between that
> particular scans and the rest from the same protocol. It stops after
the
> first iteration (default=4) and I get the following message:
>
> CV of field change: 0.000983288
> Transforming slices:............................................Done
> inputCompactField(): Incorrect number of coefficients




-- 
Best regards,

?Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com