> I am working on the pediatric template from Imaging Research Center and
> would like to use their template and apriori images in SPM2. As the format
> of these images is not in MINC format, so I used the rawtominc to get them
> converted. The following is the command I used.
The formats do not necessarily need to be MINC. They could all be Analyze
format. The problems arise if you mix Analyzr and MINC (e.g. a MINC
template, with an Analyze brain mask).
> rawtominc -transverse -byte -unsigned -range 0 255 -real_range 0 1 -orange
> 0 255 -xstep 1 -ystep 1 -zstep 1 -xstart -91 -ystart -127 -zstart -73
> -xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1 -nomodality CCHMC2_fp.mnc 182
> 218 182 < CCHMC2_fp.img
>
> {the above was cut and paste from one of the emails in SPM Archive and I
> changed the file name)
>
> I did get a converted image "CCHMC2_fp.mnc". But, they have different
> origins and intensity values when using Display to check. The information
> from the Display function of these two images is:
>
> CCHMC2_fp.img
>
> Dimension :182x218x182
> DateType : uint8
> Intensity :Y=3467.16X
> Voxel size :1x1x1
> Origin :91, 127, 73
>
> CCHMC2_fp.mnc
>
> Dimension :182x218x182
> DateType : uint8
> Intensity :Varied
> Voxel size :1x1x1
> Origin :92, 128, 74
>
> Do you have any idea what went wrong in the rawtominc command?
I don't actually test a lot of the code I send to the list, so there are
occasional errors.
First the origin. This is specified by -[xyz]start.
Try changing from "-xstart -91 -ystart -127 -zstart -73" to
"-xstart -92 -ystart -128 -zstart -74" or possibly to
"-xstart -90 -ystart -126 -zstart -72"
The intensity scaling is determined by:
-range 0 255 -real_range 0 1 -orange 0 255
You may need to change this to:
-range 0 255 -real_range 0 mx -orange 0 255
where mx is the scalefactor*255
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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