[MINC-users] mincreshape -dimsize

[Andrew Janke]

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
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