[BIC-announce] minc hackathon Dec 17-21

[D. Louis Collins]

thanks - we'll start around 9 and go until we are tired - say 4:30-5pm EST.

-L

On 2013-05-22, at 7:42 AM, Nicolas <n.guizard at gmail.com> wrote:

> Hi Louis,
> Just to let you know that you forgot to mention the starting time in your email. But you mentioned 9am yesterday. 
> Nicolas
> 
> Sent from phone
> 
> 
> Le 2013-05-21 à 16:19, "D. Louis Collins" <louis.collins at mcgill.ca> a écrit :
> 
>> Hi all,
>> 
>> We will be hosting our second MINC/ITK Hackathon on wednesday, May 22 (tomorrow).  Luis Ibanez, Matt McCormick and Xiaoxiao Liu will be here in person.   This is a followup meeting to our successful hackathon last December.  The physical location will be in room 123 of the new North Wing of the MNI. We'll set up a google hangout for others that can't join physically.
>> 
>> Ideas for the hackathon:
>> 
>> 1. The MINC-to-ITK integration is mostly done, but following things are still missing:
>> 
>> -  Writing out of floating point data to a minc file with slice normalization (right now the whole volume normalization is used)
>> 
>> - There is no support of reading minc1 files, right now it just causes the reader to produce an Exception of unsupported file format. We could try running mincconvert binary (if available on the system) to convert minc1 file to minc2 format in temp directory
>> 
>> - Support for reading and writing transformations files (xfm) is there, but right now only linear and grid transformations are supported (no support for thin-plate-spline). Also, minc xfm io library provides automatic support for forward and inverse transformation, this is not quite the same as the inverse in CompositeTransform in ITK - maybe we could take a look at that.
>> 
>> - Metadata information from MINC IO  stored in a format specific for MINC reader , perhaps it could be advantageous to standardize it across different IO modules. 
>> 
>> - Set of tests for MINC IO and MINC XFM IO might be revisited to account for all feasible combinations of data types and sources (i.e. DTI data, fMRI data, etc ). 
>> 
>> 2. mni_autoreg package ( the tool that provides linear and non-linear registration tool) is now being reworked as a library by Robb Brown : https://github.com/robb-brown/mni_autoreg/tree/lib-dev , perhaps it could be worthwhile to have it interface with ITK ?
>> 
>> 3. Patch-based segmentation and denoising 
>> 
>> - Independently from PatchBasedDenoisingImageFilter class in ITK, we have been working on implementing methods from " Patch-based segmentation using expert priors: Application to hippocampus and ventricle segmentation." : http://www.hal.inserm.fr/inserm-00541534/en/   maybe we can work on putting it in Insight journal? 
>> 
>> 4- dashboard fest and/or an adopt a bug session!
>> 
>> Please forward to anyone you think might be interested. 
>> 
>> -Louis
>> 
>> 
>> D. Louis Collins, PhD        McConnell Brain Imaging Center
>> Professor                    Montreal Neurological Institute
>> Neurology & Neurosurgery    WB-314
>> Biomedical Engineering        3801 University St.
>> louis.collins at mcgill.ca        Montreal, Quebec.
>> voice: (514)-398-4227/8554    CANADA               H3A 2B4
>> Fax:   (514)-398-2975
>> http://www.bic.mni.mcgill.ca/PeopleFaculty/CollinsDLouis
>> 
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