[accessibleimage] Re: tactile and auditory representations of neuroimaging d

Hi again,
There is something called XNAT (The Extensible Neuroimaging Archive Toolkit ), perhaps you are familiar with it. It is also an XML
From what I can tell it has a viewer, PLEXI (PLugin EXtensible Image) Viewer  where it gives low resolution images. Question is if they can be embossed out with a Tiger. Would image so.
The program is free and open source.
There is also a discussion group

XNAT http://www.xnat.org/index.html

PLEXI  Viewer  http://www.xnat.org/docs/indepth_viewer.html
Discussion   http://groups.google.com/group/xnat_discussion

XNAT
The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface. A more detailed description of XNAT can be found here.
The XNAT project is a joint venture that includes people and support from Washington University, Harvard University, Howard Hughes Medical Institute, and the Biomedical Informatics Research Network. Contact us for more information or to join the development effort.

History
XNAT has now been deployed in the ADRC for several years. Recognizing that many laboratories face similar challenges, XNAT has been made a free and open source project. Laboratories across the United States, including at Washington University, Harvard Univeristy, Massachusetts General Hospital, and the National Institutes of Health, have adopted XNAT as their data management platform, and the Biomedical Informatics Research Network (BIRN) has adopted XNAT as a standard component in its informatics repertoire.

Regards,
Lisa


accessibleimage@xxxxxxxxxxxxx skrev 29. juni 2007 kl. 13:06 +0000:
Hi,
Would think that there might be a XML for neuroimaging. There is a mark up language for making maps called GML, Geography Markup language.
There is SVG, but a XML specifically for neuroimaging would, I would think, be more efficient which would then could also include SVG for tactile production.

Just googled and found a link to A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels
http://www.springerlink.com/content/qh4223m0h175672x/

 
Abstract With the increased frequency of multisite, large-scale collaborative neuro-imaging studies, the need for a general, self-documenting framework for the storage and retrieval of activation maps and anatomical labels becomes evident. To address this need, we have developed and extensible markup language (XML) schema and associated tools for the storage of neuro-imaging activation maps and anatomical labels. This schema, as part of the XML-based Clinical Experiment Data Exchange (XCEDE) schema, provides storage capabilities for analysis annotations, activation threshold parameters, and cluster and voxel-level statistics. Activation parameters contain information describing the threshold, degrees of freedom, FWHM smoothness, search volumes voxel sizes, expected voxels per cluster, and expected number of clusters in the statistical map. Cluster and voxel statistics can be stored along with the coordinates, threshold, and anatomical label information. Multiple threshold types can be documented for a given cluster or voxel along with the uncorrected and corrected probability values. Multiple atlases can be used to generate anatomical labels and stored for each significant voxel or cluter. Additionally, a toolbox for Statistical Parametric Mapping software (http://www. fil.ion.ucl.ac.uk/spm/) was created to capture the results from activation maps using the XML schema that supports both SPM99 and SPM2 versions (http:/nnbirn.net/Resources/Users/ Applications/xcede/SPM_XMLTools.htm). Support for anatomical labeling is available via the Talairach Daemon (http://ric.uthcsa. edu/projects/talairachdaemon.htm1) and Automated Anatomical Labeling (http://www. cyceron.fr/freeware/).

Regards,
Lisa




accessibleimage@xxxxxxxxxxxxx
 skrev 29. juni 2007 kl. 12:18 +0000:
Hi All,

In an earlier conversation with Nayab (off-list) I was intrigued by the fact
that the neuroimaging software can output the digital data on which the
coloured topographical brain images are based. This seems to be in the form
of an x-y coordinate table, basically listing what value is located at each
point in a 2D "brain slice". Essentially this could be thought of as a pixel
map of a slice of brain. It's also logically similar to the kind of
geographical data stored in a GIS, like the one that Josh Miele is drawing
on for his automatically generated road maps
(http://www.ski.org/Rehab/TMAP/about.html). In Nayab's case, however, what
would be needed is a representation of regions/areas, possibly represented
by different tactile textures or by some form of tactile greyscale, rather
than representation of lines and points as in Josh's solution.

The question occurs, then, whether it might be possible to use the
coordinate data to generate a tactile image more directly, rather than
trying to process a colour image file (jpeg or whatever it might be) into
tactile form. I would assume that the digital coordinate data provides a
potentially much more flexible basis for the generation of tactile images,
including the possibility of labelling the regions in some way (i.e. by
registering the coordinate information against some map of brain anatomy).

I would be interested in this as a more general issue, because I think we'd
all agree that we need to work towards flexible ways of converting digital
spatial information into tactile formats. For instance, a solution to
Nayab's problem would also be handy for blind students and practitioners in
geography, who need to be able to render digital spatial information in
tactile form.

All the best,

Simon


On 28/6/07 16:43, "N.Begum" <begumn1@xxxxxxxxxxx> wrote:

> Hi John,
>
> Thank you for your email.
> We¹re currently trying to get samples of brain images to tiger embosser
> manufacturers to assess how much detail I can get from them, but this
> technology looks really promising.  With regard to the IVEO technology,
> we¹re not really sure how useful this might be, as I¹m trying to find ways
> to access neuroimaging as independently as possible, and my understanding
> of the IVEO touchpad is that I¹d require sighted assistance to assign
> labels and descriptions to an image.  The VOICE software also sounds very
> interesting, and we¹ll definitely try this too, but I was just wondering
> how easy it might be to build up a mental image spatially.  With a line
> graph for example, is it possible to quantify or work out the scale, e.g.
> from the no. of seconds the tone sounds for.   We¹ve also come across the
> Audiographing calculator-do you think this might be more useful to us?
> Also, do you happen to know how far research has managed to get in terms
> of producing tactile diagrams in real-time?
>
> Many thanks
>
> Nayab
>
>
>
>
>
>
>> Hello Nayab.   The IVEO technology developed by ViewPlus and used with a
>> Tiger embosser has much of the functionality that you need.  Ability to
>> identify color and other image attributes is the subject of an IVEO
>> expansion research and development project that is now underway, and it is
>> working beautifully in our research applications.  The commercial version
>> is
>> some way from introduction, but I'd be happy to work with you basically as
>> a
>> participant in this development.  I suggest you read over the info on IVEO
>> on the ViewPlus web site, and in particular read some of the research
>> articles linked from http://www.viewplus.com/abstracts/ to learn what IVEO
>> is and can do for you now.  Then please write me, and we can discuss the
>> current research project and how it might help solve your problems.
>>
>> Peter Meijer has also written about the innovative VOICe technology that
>> he
>> has developed.  I'd be interested to know whether VOICe could be used in
>> combination with IVEO for things like neuro-imaging.  My guess is that
>> IVEO
>> and VOICe would complement each other beautifully.  And I'll bet that
>> Peter
>> would be happy to help out.  Maybe he'd like to comment.
>>
>> John Gardner
>>
>>
>>
>> -----Original Message-----
>> From: accessibleimage-bounce@xxxxxxxxxxxxx
>> [mailto:accessibleimage-bounce@xxxxxxxxxxxxx] On Behalf Of N.Begum
>> Sent: Wednesday, June 27, 2007 7:46 AM
>> To: accessibleimage@xxxxxxxxxxxxx
>> Cc: barnesgr@xxxxxxxxxxx
>> Subject: [accessibleimage] tactile and auditory representations of
>> neuroimaging data
>>
>> Hello,
>>
>> My name is Nayab Begum, I'm a psychology student at Aston university and
>> registered blind.
>> I am hoping to pursue a career in neuroimaging, and currently trying to
>> find
>> ways to make the technique more accessible.  This will involve being able
>> to
>> access complex brain images in colour as well as graphs.
>> I was wondering whether anyone might be able to recommend the most
>> appropriate assistive technology for tactile diagrams?  We've been looking
>> into electronically refreshable devices, but there doesn't seem to be
>> anything on the market, and we're not sure it would provide sufficient
>> level
>> of detail.  From our research, the most advanced technology seems to be
>> the
>> tiger embosser, although this also seems to have its limitations.
>> If anybody knows about the phantom device, and if it is sold in the UK,
>> that
>> would also be very helpful.
>> Another option we're looking into is converting images to sound-does
>> anyone
>> have any experience with this?
>> Also, for the data analysis, we use matlab and scientific linux.  We're in
>> the process of installing Ubuntu to use the orca speech software, but
>> we're
>> not really sure how much i twill be able to read.  If anyone has
>> experience
>> with using linux with a Braille note taker, I'd also be really interested
>> to
>> know how compatible it is.
>>
>> We would be really grateful for any advice
>>
>> Many thanks
>>
>> Nayab
>>


Lisa Yayla
Huseby Kompetansesenter
Oslo Norway
lisa.yayla@xxxxxxxxxx

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