[MINC-users] mincreshape problem

[Vladimir S. FONOV]

Hello,


it looks like this minc file from MIPAV doesn't have variable image-min defined, i.e if you do h5ls -r on a well-defined minc2 file it will show you something like that:

/                        Group
/minc-2.0                Group
/minc-2.0/dimensions     Group
/minc-2.0/dimensions/xspace Dataset {SCALAR}
/minc-2.0/dimensions/yspace Dataset {SCALAR}
/minc-2.0/dimensions/zspace Dataset {SCALAR}
/minc-2.0/image          Group
/minc-2.0/image/0        Group
/minc-2.0/image/0/image  Dataset {193, 229, 193}
/minc-2.0/image/0/image-max Dataset {193}
/minc-2.0/image/0/image-min Dataset {193}
… etc …

so, you file probably have /minc-2.0/image/0/image-min bit missing…
which is needed to correctly interpret the intensity information in the file.


On 2012-12-14, at 8:27 PM, Soren Christensen <sorench at gmail.com> wrote:

> Hi,
> I am trying to fix up some MINC files that were written by MIPAV, for some
> reason some of these files have extra slices and displacement of the ROI.
> In plane resolution is the same.
> What I am stuck with is the followoing mincresample behaviour:
> 
> file: a.mnc
> image: signed__ short -32768 to 32767
> image dimensions: zspace yspace xspace
>    dimension name         length         step        start
>    --------------         ------         ----        -----
>    zspace                     26            5     -77.0989
>    yspace                    256      -0.9375      128.406
>    xspace                    256      -0.9375      121.591
> 
> 
> file: b.mnc
> image: signed__ short -32767 to 32767
> image dimensions: zspace yspace xspace
>    dimension name         length         step        start
>    --------------         ------         ----        -----
>    zspace                     27            5     -77.0989
>    yspace                    256      -0.9375      128.406
>    xspace                    256      -0.9375      121.591
> 
> 
> So file a has one slice less than b, but spatial info match. So I'd like to
> resample b.mnc like a, in the hope that the top slice is irrelevant ()
> 
> mincresample -like a.mnc b.mnc b_likea.mnc
> (from miattputstr): Function 'dimrename' not implemented
> Transforming slices:..........................Done
> 
> #> mincinfo a.mnc b_likea.mnc
> file: a.mnc
> image: signed__ short -32768 to 32767
> image dimensions: zspace yspace xspace
>    dimension name         length         step        start
>    --------------         ------         ----        -----
>    zspace                     26            5     -77.0989
>    yspace                    256      -0.9375      128.406
>    xspace                    256      -0.9375      121.591
> 
> 
> file: b_likea.mnc
> image: signed__ short -32767 to 32767
> image dimensions: zspace yspace xspace
>    dimension name         length         step        start
>    --------------         ------         ----        -----
>    zspace                     27            5     -77.0989
>    yspace                    256      -0.9375      128.406
>    xspace                    256      -0.9375      121.591
> 
> 
> So b_likea.mnc is not what expect it to be (26 slices). The file seems
> broken:
> 
> Display b_likea.mnc
> Input b_likea.mnc
> HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 0:
>  #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
>    major: Dataspace
>    minor: Out of range
> (from miicv_attach): Can't read dataset /minc-2.0/image/0/image-min
> (from miicv_attach): Can't read variable ID# 1
> miicv_attach: MINC package entry point
> HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 0:
>  #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
>    major: Dataspace
>    minor: Out of range
> (from miicv_attach): Can't read dataset /minc-2.0/image/0/image-min
> (from miicv_attach): Can't read variable ID# 1
> miicv_attach: MINC package entry point
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> (from miicv_get): ICV is not attached
> 
> 
> Any suggestions to what is happening herE?
> 
> Soren
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

---
Best regards,

Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info