Difference between revisions of "DBP:Harvard:Software:Minutes:9"

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m (Update from Wiki)
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Raul,
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''Agenda for 9/7/05''
  
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I put a case from the outside world in /projects/schiz/guest/sylvain/data/For_Markd
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<br />'''2 ROI method for DTI fiber tracking''' (details [[DBP:Harvard:Software:Bugs:2ROI|here]])
  
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Here is the info about the case:
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* Lauren's module
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** previous bug fixed (pay attention to 2nd label map color)?
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** does it track in both directions (from ROI1 to 2, and 2 to 1)?
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** ideas... procedure for isolating 2 separate ROIs from existing labelmap?
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** using Matlab to measure FA/Trace, etc: do we know how to do this?
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* Raul's module
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** Do we want to meet with him and make sure we're using the module correctly?
  
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TR 6000 ms, TE 100 ms, 128x128 matrix, 320 mm FOV, 8/8 RectFOV, _b_-value=1000 s/mm2 , 8 non-collinear gradient orientations, 7 averages, 19 slices, 5 mm slice thickness, no skip, 2.5x2.5 mm pixel size
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<br />'''Fiber clustering''' (details[[DBP:Harvard:Software:Wish:Cluster_3-29-05|here]])
  
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The orientation is axial IS, endianess Big.
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* Lauren: updated draft of letter for paper?
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** images for paper: more fornix pics (Mark)
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* other ideas for clustering...
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** "backtracking" method on corpus callosum
  
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I stripped the header and loaded the files in slicer and they look fine.
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<br />'''DTI case for Lynn DeLisi''' (details from Sylvain to Raul [[DBP:Harvard:Software:Minutes:9-7-05:DeLisi|here]])
  
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I tried creating a protocol but I am not sure hoe to do this with the ordering of the files which is a mix of slice interleaved and volume interleaved:
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* Does this need to be taken care of soon?
  
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01-07: 7 T2 scans of the same slice
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<br />'''Stephan's LSDIrecon code''' (details [[DBP:Harvard:Software:Wish:Stephan_code_8-24-05|here]])
  
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08-14: 7 T2 scans of the next slice
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* Scott: any updates?
  
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do this 19 times...
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<br />'''Background noise in DTMRI scalar measures''' (details [[DBP:Harvard:Software:Bugs:Noise|here]])
  
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--
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* Where did we leave off with this?
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** Is this related to Scott's work with Stephan's code??
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** Gordon? mask??
  
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134-140: 7 * (0.000 1.0000 0.0000) gradient of the same slice
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<br />'''Higher resolution scans on 3T''' (details [[DBP:Harvard:Software:Wish:3T_8-24-05|here]])
  
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141-147: 7 * (0.873 0.488 0.000) gardient of the same slice
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* KangUk: any updates?
  
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do this 19 times...
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<br />'''Old Wishes'''
  
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--
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* review [[DBP:Harvard:Software:Wish|here]]
  
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There are a total of 8 gradient directions:
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<br />
  
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0.000 1.0000 0.000
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----
  
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0.873 0.488 0.000
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<br />'''Still being worked on...'''
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0.266 -0.2 0.942
 
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-0.7 0.678 0.224
 
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-0.599 0.119 0.792
 
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-0.324 -0.686 0.651
 
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0.265 0.631 0.729
 
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0.876 -0.229 0.425
 
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<br />
 
  
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Let me knwo if you can help. I am out of town next week so there is no rush to do this.
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* Coronal AP cases and fiber tracking: The concensus seems to be that everything should be fine with this cases, but Mark will do fiber tracking on corpus callosum and show images next week.
  
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-S
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* Steve's updated VolumeMath code is in slicer_lmi. Mark is working on testing cases 1) against Stephan's LSDIrecon data, and 2) using the "Include Zeros" option that Steve added

Revision as of 13:19, 18 December 2006

Home < DBP:Harvard:Software:Minutes:9

Agenda for 9/7/05


2 ROI method for DTI fiber tracking (details here)

  • Lauren's module
    • previous bug fixed (pay attention to 2nd label map color)?
    • does it track in both directions (from ROI1 to 2, and 2 to 1)?
    • ideas... procedure for isolating 2 separate ROIs from existing labelmap?
    • using Matlab to measure FA/Trace, etc: do we know how to do this?
  • Raul's module
    • Do we want to meet with him and make sure we're using the module correctly?


Fiber clustering (detailshere)

  • Lauren: updated draft of letter for paper?
    • images for paper: more fornix pics (Mark)
  • other ideas for clustering...
    • "backtracking" method on corpus callosum


DTI case for Lynn DeLisi (details from Sylvain to Raul here)

  • Does this need to be taken care of soon?


Stephan's LSDIrecon code (details here)

  • Scott: any updates?


Background noise in DTMRI scalar measures (details here)

  • Where did we leave off with this?
    • Is this related to Scott's work with Stephan's code??
    • Gordon? mask??


Higher resolution scans on 3T (details here)

  • KangUk: any updates?


Old Wishes



Still being worked on...

  • Coronal AP cases and fiber tracking: The concensus seems to be that everything should be fine with this cases, but Mark will do fiber tracking on corpus callosum and show images next week.
  • Steve's updated VolumeMath code is in slicer_lmi. Mark is working on testing cases 1) against Stephan's LSDIrecon data, and 2) using the "Include Zeros" option that Steve added
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