[MINC-users] ana2mnc problem

[Robert VINCENT]

Hi Catherine,

The revised (sagittal) files seem to be in floating-point format, whereas
the originals were in short integer format.  Ana2mnc calls rawtominc,
which doesn't deal with byte-swapping floating-point datatypes.

What was the difficulty in reorienting the MINC files?  That should have
been pretty straightforward.  I'll be happy to help if you're willing to
give that approach another try.

	-bert

On Mon, 24 Jan 2005, Catherine Ogilvie wrote:

> Andrew, the new ana2mnc program you sent me worked wonderfully.
>
> However, I then needed the images transformed into sagittal orientation. I
> tried to use the minc programs suggested by everyone on minc-users, but when I
> had a lot of difficulty I had them transformed into sagittal while in .hdr
> .img format by the group sending them to me. Now when I run the dimension
> transformed .hdr .img files on the ana2mnc program it does not turn out a
> readable format, with the repeated warning output:
>
> Warning: you specified -swap_bytes, but I can't swap this type if input
>
> I'm not sure what's happening.
>
> When I convert to minc, the dimensions of the images in original axial form
> are:
>
> image: signed__ short 0 to 32767
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                     64      2.72727     -87.2727
>     yspace                    256     0.859375         -110
>     xspace                    256    -0.859375          110
>
> The dimensions in transformed sagittal form, when converted to minc, are:
>
> image: signed__ float -1.6814541463787951101e+38 to 3.3836776830158255673e+38
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                    256     0.859375         -110
>     yspace                    256     0.859375         -110
>     xspace                    256    -0.859375          110
>
> not sure if this makes a difference, but this is the one that's giving me the
> errors and pixelated output.
>
> Thanks for your help.
> Catherine Ogilvie
>
>
> >===== Original Message From Andrew Janke <andrew_janke@iinet.net.au> =====
> >On Wed, 8 Dec 2004, Catherine Ogilvie wrote:
> >
> >> Hi. I'm trying to use ana2mnc for the first time. I have had a .img and
> .hdr
> >> pair sent to me from another lab which uses analyze. When I run ana2mnc I
> get
> >> this:
> >>
> >> ana2mnc: sizeof header: 1543569408
> >> ana2mnc: Hrm, attempting byte-swapping on ANATcw.24_02_03_2.fid_001.hdr
> >> ana2mnc: No x origin info found, guessing..
> >> ana2mnc: No y origin info found, guessing..
> >> ana2mnc: No z origin info found, guessing..
> >>
> >> and a very strangely pixelated output.
> >
> >I'm guessing that when you tranferred the data, the header was byte swapped
> and
> >the data wasn't.
> >
> >Try this version of ana2mnc
> >
> >    http://www.bic.mni.mcgill.ca/~rotor/distro/ana2mnc-1.3c
> >
> >using the -swap_data option.
> >
> >If this works, I'll add this feature into the next release of ana2mnc
> >
> >
> >--
> >Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor)
> >Australia->Brisbane            H: +61 7 3390 6332  || M: +61 4 2138 8581
>
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