Difference between revisions of "DBP:Harvard:Software:Minutes:4"

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== DTI Meeting Minutes | April 19, 2006 ==
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== DTI Meeting Minutes | April 26, 2006 ==
  
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<br /> Present: Mark, Gordon, Katharina, Sylvain, Marty, CF, Gudrun, Marek, Doug
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<br /> Present: Doug, Marc, Katharina, Sylvain, Kang Uk, Gordon, CF, Marek, Gudrun
  
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<br />'''Visitors tomorrow 4/20/06:'''
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<br />
  
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* Jim Kennedy and Aristotle will be visiting from Toronto tomorrow at 2:00. They have a strong background in genetics and are interested in our DTI research
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* Slicer
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* Marek, Sylvain, Marc will be showing DTI work in the PNL, Gordon will also contribute if available
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** Slicer26 should be able to read NRRD DWIs now
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** doDTI gives you mean FA, would be nice to display this in Slicer somewhere
  
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<br />'''Progress on new protocol:'''
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<br />
  
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* Marek needs to be added to an IRB, which will take a week to be processed
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* New protocol: scanning today?
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* We have 5 volunteers ready to be scanned once IRB approval is worked out
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** required that a licensed MD approve every scan
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** sequence will be DICOM files, probably same format as before, same procedure for downloading
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** Marek meeting with Nan-Quei at 1:30 today at the SPL to talk about the protocol
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** Will try multiple scans varying b-value and number of directions
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*** Will try 750 and 1000 with minimum of 32 directions; also try 50 directions
  
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<br />'''Anterior Commissure boundaries:'''
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<br />
  
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* Gordon has a method to delineate the boundary of the AC based on 2nd-derivative inflection points; he will create maps of these boundaries overlaid with the 'red' channel from the ColorByOrientation scalar maps for chronic/male dataset, and give them to PNL for drawing
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* Anterior Commissure
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** would be nice to have an extra scalar map with orientation overlayed with the output of this method
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** Gordon will finish creating these maps and send to Sylvain
  
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<br />'''DoDTI vs. Slicer'''
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<br />
  
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* Tractography in DoDTI and Slicer produce very different results, probably because of different seeding methods (DoDTI seeds first from a white matter atlas then prunes based on ROI, Slicer seeds directly from ROI labelmap. PNL will try to do seeding in Slicer from white matter atlas--but this involves a lot of steps and would be helpful to have a streamlined process similar to that in DoDTI.
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* Cingulum Bundle histograms of FA/Mode
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** note that people tend to overestimate how linear the ROI will be.. mostly orthotropic
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** now that we know that anisotropy is a bi-variate quantity, still need to answer the question about how to do statistics on this; non-parametric tests?
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** would be helpful to have comparison of different white matter ROIs, plotted in this space
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*** Corpus callosum, cingulum bundle, STG white matter, STG gray matter, CSF; these ROIs will be sent to Gordon
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<br />
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* Kang Uk - problem with tensor coregistration?
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** script was updated by Mattan in slicer-nightly, but still doesn't seem to be working
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** will try a basic co-registration of two tensor sets in the same direction

Revision as of 13:19, 18 December 2006

Home < DBP:Harvard:Software:Minutes:4

DTI Meeting Minutes | April 26, 2006


Present: Doug, Marc, Katharina, Sylvain, Kang Uk, Gordon, CF, Marek, Gudrun


  • Slicer
    • Slicer26 should be able to read NRRD DWIs now
    • doDTI gives you mean FA, would be nice to display this in Slicer somewhere


  • New protocol: scanning today?
    • required that a licensed MD approve every scan
    • sequence will be DICOM files, probably same format as before, same procedure for downloading
    • Marek meeting with Nan-Quei at 1:30 today at the SPL to talk about the protocol
    • Will try multiple scans varying b-value and number of directions
      • Will try 750 and 1000 with minimum of 32 directions; also try 50 directions


  • Anterior Commissure
    • would be nice to have an extra scalar map with orientation overlayed with the output of this method
    • Gordon will finish creating these maps and send to Sylvain


  • Cingulum Bundle histograms of FA/Mode
    • note that people tend to overestimate how linear the ROI will be.. mostly orthotropic
    • now that we know that anisotropy is a bi-variate quantity, still need to answer the question about how to do statistics on this; non-parametric tests?
    • would be helpful to have comparison of different white matter ROIs, plotted in this space
      • Corpus callosum, cingulum bundle, STG white matter, STG gray matter, CSF; these ROIs will be sent to Gordon


  • Kang Uk - problem with tensor coregistration?
    • script was updated by Mattan in slicer-nightly, but still doesn't seem to be working
    • will try a basic co-registration of two tensor sets in the same direction
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