MINC format

Questions about BrainVisa usage and installation

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Jean-Francois Mangin
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MINC format

Post by Jean-Francois Mangin »

Christophe Grova said:

j ai qques problemes pour convertir en GIS des cartes T IRMf qui sont en MINC .... en effet l outil que tu m avais file , que j ai un peu modifie pour mes besoin (qques Flips !) ... ne sort que des donnees en 16 bits or la il faudrait que je sorte du flottant ... d ou deux questions :

- as tu deja fait evolue cette outil (minc2gis) pour qu il sorte du flottant ?
- sinon, je veux bien le faire ...mais pour cela il me faudrait tes sources, car je n ai que l executable VipConvertmincTOgis, et il me faudrait qques pistes ou le source, car visiblement cet outil fait plus qu un simple minctoraw.

Hi Christophe,
we would appreciate a lot if you
could integrate the MINC format in brainVISA
framework. We plan that for a long time but
never find time. The VipConvertmincTOGIS
was an attempt I did while working in the MNI
in 2001, before the advent of brainVISA first release.
I get so confused by the multiple layers of
MINC IO, I finally gave up doing something
generic. I think we should forget about this code now.
The right way to proceed should be something like:

Download sources of AimsData, which relates to the IO
system of Anatomist and all the AimsSomething command lines
used by brainVISA (unfortunally, the C-based Vip library relies
on an out of date IO system, but brainVISA can convert
anything in GIS format before feeding Vip Command lines).
AimsData includes a system of modules, which allows the addition of
new formats as long as the corresponding dynamic library
is somewhere in the path of the user (Denis Rivière did this
nice stuff). I think you should put there
some kind of wrapper towards mincIO, I guess something
above volumeio library. The simplest way to do it would
be to ask Jason Lerch to give you access to his C++
encapsulation of volumio.

Home you will manage to do that.

Jeff
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riviere
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Post by riviere »

Hi,

If the IO layers and plugin system of Aims seems too complex for you (or too poorly documented), you can just write some read() and write() functions which fills an AimsData object, and I can do the plugin in aims myself.

Denis
grova
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Location: Montreal Neurological Institute

MINC converter

Post by grova »

I will try to do something ... but where are the source I should download and compile to look at that ?
There are so many pack that you could download on the site ... I don t know what to choose


Jeff, are the source of your VipConvertmincTOgis included somewhere ?
It may be a good step to start with ...because at least you solved the problem of orientation for minc axial files

Thanks in advance , Christophe
***************************
Christophe Grova, PhD
PostDoc - EEG department
Montreal Neurological Institute, McGill University
email : christophe.grova@mail.mcgill.ca
tel : (514) 398 2184
fax : (514) 398 8106
***************************
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riviere
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Post by riviere »

You can get the sources on the download section of the web site: http://brainvisa.info/downloadpage.html. The sources of the latest stable release are those from the 2.3 package.
You need aimsdata-2.13, graph-1.16, cartobase-1.1, and the build tools: build-config, configure and maker. ecat and vidaIO plugins are optional.
Compilation instructions on http://brainvisa.info/compilation.html are a bit outdated, but basically you need to untar the source packages in the same directory, make the compilation tools accessible in your PATH, and do a:

Code: Select all

build-config --build aimsdata
This should configure and build everything needed. For more information and options of build-config, look at http://brainvisa.info/build.html
As you will soon see, there is quite a lack of documentation. However you can build a coarse doc using doxygen: doxygen is inclued in all good linux distributions and builds HTML documentation pages from a set of .h files. If you build this doc, you will find a small doc on the IO system of Aims (this is the only part which has a bit of doc, how lucky you are...)


Good luck...
Denis
Olivier_Colliot
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Post by Olivier_Colliot »

Hi Christophe (and everyone!)

Until now, I only imported 16bit data and the Vip command was perfect for that.
But I will be interested to import float as well in the near future.

If you want, I can try to give you a little help with this.
I don't know much about minc but want to learn a bit of Aims. So it could be a good occasion to get into it

Olivier

(email me : colliot@bic)
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

I will be in Montreal the first week of june.
If it is not done at that point, I may try to discuss
about that with you. Anyway, we could have a beer together
arounf that time:-)
Jeff
PS I will send you VipMinc... sources tomorrow.
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Jean-Francois Mangin
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work in progress

Post by Jean-Francois Mangin »

Just a couple of information.
Olivier Coliot did a great job during the last weeks.
Thanks to him and Denis, Anatomist and BrainVISA
should be able to read Minc-1 format in the next release.
Jeff
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