[MINC-development] MINC format converters

[Andrew Janke]

On Mon, 24 Mar 2003, Colin Holmes wrote:

> I'd like to validate a list of minc file format
> converters currently being collected by the NIH's
> NIFTI Data Format Working Group.  Please take a quick
> look at the following list of converters and if you
> know of an addition, please reply to me
> directly with the following information about it:
>
> Input format name:   	(standard file extension is great too)
> Output:  			(just .mnc or is there a minc -> .format? )
> URL/ Download site:	(where to get it)
> Development Info:		(author?)
> Dependencies:		(needs some other package?)
> Comments:			(whatever you have to say about it)
> Suggested By:		(who you are, email address is fine)


===ana2mnc|mnc2ana|spm2mnc|mnc2spm|ana_show===
Input format name:   	Analyze
Output:  		.mnc
URL/ Download site:	http://www.cmr.uq.edu.au/~rotor/software/
Development Info:	Andrew Janke (rotor@cmr.uq.edu.au)
Dependencies:		Perl
Comments:		has become a bit of a dog. (see below)
Suggested By:		rotor@cmr.uq.edu.au

===unc2mnc===
Input format name:   	UNC
Output:  		.mnc
URL/ Download site:	http://www.cmr.uq.edu.au/~rotor/software/
Development Info:	Andrew Janke (rotor@cmr.uq.edu.au)
Dependencies:		Perl
Comments:		UNC is of BAMM/XBAMM UCL fame.
Suggested By:		rotor@cmr.uq.edu.au

===gis2mnc===
Input format name:   	gis
Output:  		.mnc
URL/ Download site:	none, mail me if you want it
Development Info:	Andrew Janke (rotor@cmr.uq.edu.au)
Dependencies:		Perl
Comments:		Is largely untested, GIS is the format
                          used anatomist (the sooper-dooper french
                          sulcal identification suite of tools)
                        NB: the french have their own mnc2gis converter
                          that uses volume_io for the conversion.
Suggested By:		rotor@cmr.uq.edu.au

===mif2mnc===
Input format name:   	mif4
Output:  		.mnc
URL/ Download site:	BIC CVS
Development Info:	Andrew Janke (rotor@cmr.uq.edu.au)
Dependencies:		Perl
Comments:		MIF4 is used/developed by UBC,
                          docco for this converter was kindly provided by
                          Andrew Riddenhough.
Suggested By:		rotor@cmr.uq.edu.au

===m2f2mnc===
Input format name:   	m2f
Output:  		.mnc
URL/ Download site:	BIC CVS
Development Info:	Louis Collins
Dependencies:		Perl
Comments:		M2F is an old format of UBC's
Suggested By:		rotor@cmr.uq.edu.au

===pvconv===
Input format name:   	Bruker Paravision
Output:  		.mnc
URL/ Download site:	http://www.mrc-cbu.cam.ac.uk/Imaging/pvconv_pod.html
Development Info:	Matthew Brett and Andrew Janke
Dependencies:		Perl
Comments:		Bruker "format" of Paravisino ilk.
                          this is primarily a PV->analyze converter with
                          experimental MINC support.  (-outtype=minc)
Suggested By:		rotor@cmr.uq.edu.au


There are also of course the siemens/GE/phillips/scx/ecat converters that you
would know about already.

> Known MINC converters & input formats:
>
> 3dAFNItoMINC
> 3dMINCtoAFNI
> ana2mnc, mnc2ana (UCLA's analyze to minc-ers)

Interesting....  (got a URL?)  I have become quite despondent as of late with
"ANALYZE" to minc converters simply because of the veritable plethora of
versions of analyze format that appear to exist, and when you add SPM into the
mix it just get's even more fun.

IMHO SPM "ANALYZE" should die a painfull death.  Or at least not purpote itself
to be "analyze" which it is not.

> Suspected format converters -- please point me to:
>
> STIMULATE <-> MINC
> VIFF <-> MINC
> minc <-> 3D Tiff

use mincpik.  (it uses Imagemagicks convert).

> anything else NIFTI should know about?

MINC will rule the earth.

On this note i have recently began work on a all-singing all-dancing converter
myself that will use XML as a base format as per ImageMagicks MIFF.  I have not
yet found a suitable candidate for the XML DTD but am still searching.  The
reason being that all the perl converters I have written share a common "$ghdr"
object that could very easily become XML.

Best part is netcdf XML converters already exist, eg: an example converted
header from a MINC file: http://www.cmr.uq.edu.au/~rotor/graagh/foo.xml

Of course WRT XML there is always http://imlib3d.sourceforge.net/ This library
supports an XML datatype so currently I am tending towards it's internal format
as a base DTD.

I'll be very interested to know the results/outcome of your little group.



--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
Work: +61 7 3365 4100 || Home: +61 7 3800 4042