[MINC-users] mincreshape -dimsize

[Soren Christensen]

Thanks Andrew!
 Yes file is MINC2 and it was exactly your 2nd point I failed toremember in
detail.
It actually does not seem to do the trick - the image comes out without a
zspace dimension if I add this option.
I used mincresample instead, and using the desired -zsize and -zstep with
no other options achieved the re-slicing I was looking for.
Let me know if you want me to do something to document the mincreshape issue

Thanks!
Soren

On Sun, Sep 20, 2015 at 4:41 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren,
>
> This could be one of two things.
>
> 1. Is this a MINC1 or MINC2 file? If the former, convert to MINC2
> first using mincconvert
>
> 2. I think what you are alluding to is "-dimrange zspace=-1" option
> that will tell mincreshape to treat a slice dimension as an image
> dimension.
>
> There has been a feature request kicking about for a long time to
> remove this behaviour as it doesn't make as much sense as it used to
> when Peter first implemented slice scaling in MINC1 but I don't think
> it's made it into the latest release as of yet.
>
>
> a
>
>
>
> On 20 September 2015 at 13:48, Soren Christensen <sorench at gmail.com>
> wrote:
> > Hi,
> >  I have an issue with mincreshape I don't understand. I guess it has to
> do
> > with trying to interpolate the slowest varying dimension:
> >
> > file: pwi_bl.mnc
> > image: signed__ float 0 to 1381.4969482421875
> > image dimensions: zspace yspace xspace
> >     dimension name         length         step        start
> >     --------------         ------         ----        -----
> >     zspace                     17            5      -38.912
> >     yspace                    128        -1.75      95.0638
> >     xspace                    128        -1.75      110.338
> >
> > u at K450$ mincreshape -dimsize zspace=49 -float -clobber  pwi_bl.mnc
> > pwi_blIP.mnc
> > Copying chunks:HDF5-DIAG: Error detected in HDF5 (1.8.15-patch1) thread
> 0:
> >   #000: H5Dio.c line 161 in H5Dread(): selection+offset not within extent
> >     major: Dataspace
> >     minor: Out of range
> > (from mivarget): Can't read dataset /minc-2.0/image/0/image-min
> > (from mivarget): Can't read variable ID# 1
> > HDF5-DIAG: Error detected in HDF5 (1.8.15-patch1) thread 0:
> >   #000: H5Dio.c line 161 in H5Dread(): selection+offset not within extent
> >     major: Dataspace
> >     minor: Out of range
> > (from mivarget): Can't read dataset /minc-2.0/image/0/image-max
> > (from mivarget): Can't read variable ID# 2
> > .................................................Done.
> >
> > The file is written but it appears incorrect with a larger Z FOV for
> > starters but it also look as if the extreme slices are simply copied
> > outwards at each end (sorry cannot post images here). Finally the image
> > appears corrupted in register and freezes up Display and the OS!
> >
> > file: pwi_blIP.mnc
> > image: signed__ float 0 to 1381.4969482421875
> > image dimensions: zspace yspace xspace
> >     dimension name         length         step        start
> >     --------------         ------         ----        -----
> >     zspace                     49          2.5      -57.662
> >     yspace                    128        -1.75      95.0638
> >     xspace                    128        -1.75      110.338
> >
> > -dimsize xspace=64 works without errors.
> >
> > I have a vague recollection Andrew Janke once explained how to deal with
> > this but I am unable to locate that post (if it ever existed).
> >
> > Thanks!
> > Soren
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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