[MINC-development] minc 2.0.14 issues

[Steve M. Robbins]

On Thu, Jan 17, 2008 at 10:34:44PM +1100, Andrew Janke wrote:
> > Just to let you know, I've recently uploaded MINC 2.0.14 to Debian.
> > There's an active project to get all kinds of medical imaging software
> > into Debian; see http://wiki.debian.org/DebianMedImaging.  FSL is in,
> > and there is interest in AFNI, Caret, and FreeSurfer.  Since the
> > latter is built on MINC, work was started on a number of BIC packages,
> > including mni_autoreg and N3.
> 
> I presume you are talking about Michael Hanke here.

Yes.  I'm glad to hear you've been in contact.


> I am more than keen to get things right upstream.  I note there are a
> number of patches in the deb build. I presume you will commit these
> upstream also? 

At present there are just three patches in Debian's package of MINC.

01_mincedit-sensible-viewer.diff simply sets the default editor to
"sensible-editor" rather than "emacs".  Since "sensible-editor" is a
Debianism (basically a script that tries VISUAL, EDITOR, then some
hard-coded fallbacks) I wasn't planning to push this upstream.  I
might suggest, though, that mincedit use $VISUAL, falling back to
$EDITOR, then something hardcoded, e.g. emacs.  Then I'd probably
remove the Debian patch.

02_testdir-runtests.diff is already in MNI's CVS tree, though for
MINC-2 only.  This is a clear bug that prevented anyone from using
"make check" or "make distcheck".  I patched it without announcing
because I'm sure it is uncontroversial.

03_mincview.diff changes the viewer from "xv" to Imagemagick's
"display".  This one should probably be applied to the MNI repository
since "xv" is nearly impossible to find these days, whereas
Imagemagick is ubiquitous.  I'm attaching the patch for comments.


> > 2. I built MINC using --enable-acr-nema for the first time, and
> > discovered that it produces a program named "extract" that simply
> > extracts bytes from the middle of the input.  Unfortunately, this name
> > clashes with a pre-existing software package that has more claim to
> > the name (http://bugs.debian.org/459834).  Fortunately, it looks to me
> > like MINC's extract can be replaced by "dd".  So I plan to solve this
> > by removing "extract" from Debian's package.  The same goes for
> > byte_swap.  Maybe they can be removed completely?  Is anyone really
> > using these tools (and can't switch to using dd)?
> 
> I would go further than this.  I see no reason as to why acr-nema
> should be a library. Berts intention here probably was noble but
> no-one else that I know of would use it that I can think of when there
> are things like dc3tools from david clunie.  My suggestion would be to
> mod the build process so that the library is not built at all.  

The easiest mod is to make it a "convenience library".  That means it
is built as a library and used to link the tools, but the library is
not installed.


> byte_swap is a little more interesting though, there was at one stage
> a byte_swap4 and a byte_swap8 I have no idea if these still exist as
> these are a tad more difficult to implement with dd.

The source tree does contain byte_swap4.c, but the tool is not
compiled nor installed.  I don't see any byte_swap8.


Cheers,
-Steve
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