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

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Raul,
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''Agenda for 9/21/05''
  
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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 />'''Comparison of LSDIrecon and DTMRI scalar measures, also including Steve's "include zeros" functionality''' (details [[DBP:Harvard:Software:Testing:DTI:Slicer|here]])
  
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Here is the info about the case:
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# Differences in FA are always <0.25% (usually much smaller)
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# Raul removed the Scale Factor, which seems to make Trace values very small compared to ADC
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#* BUT DTMRI trace values are still consistent (in relative terms) with LSDIrecon ADC, i.e., always 250X smaller
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# Including zeros (Steve's added button) did not make a difference. Does this mean 1) there is no difference, or 2) the "include zeros" button does not work?
  
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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 />'''Diffusion cases acquired Coronal AP''' (details [[DBP:Harvard:Software:Bugs:Coregistration_5-11-05|here]])
  
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The orientation is axial IS, endianess Big.
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* Fiber tracking seems to be fine on these cases
  
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I stripped the header and loaded the files in slicer and they look fine.
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<br />'''2 ROI method for DTI fiber tracking''' (details [[DBP:Harvard:Software:Bugs:2ROI|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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* I can't get it to work- please help!
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* "NOT" functionality: Raul is working on it
  
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01-07: 7 T2 scans 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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08-14: 7 T2 scans of the next slice
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* Fibertracking was done after smoothing the tensor.
  
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do this 19 times...
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<br />'''Fiber clustering''' (details[[DBP:Harvard:Software:Wish:Cluster_3-29-05|here]])
  
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--
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* fiber backtracking/corpus labeling method?
  
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134-140: 7 * (0.000 1.0000 0.0000) gradient of the same slice
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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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141-147: 7 * (0.873 0.488 0.000) gardient of the same slice
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* Marek, do we know what variables/examples she wants from us?
  
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do this 19 times...
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<br />
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--
 
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There are a total of 8 gradient directions:
 
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0.000 1.0000 0.000
 
  
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0.873 0.488 0.000
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----
  
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0.266 -0.2 0.942
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<br />'''Other issues...'''
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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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* '''Stephan's LSDIrecon code''' (details [[DBP:Harvard:Software:Wish:Stephan_code_8-24-05|here]])
  
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-S
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* '''Background noise in DTMRI scalar measures''' (details [[DBP:Harvard:Software:Bugs:Noise|here]])

Revision as of 13:55, 18 December 2006

Home < DBP:Harvard:Software:Minutes:9

Agenda for 9/21/05


Comparison of LSDIrecon and DTMRI scalar measures, also including Steve's "include zeros" functionality (details here)

  1. Differences in FA are always <0.25% (usually much smaller)
  2. Raul removed the Scale Factor, which seems to make Trace values very small compared to ADC
    • BUT DTMRI trace values are still consistent (in relative terms) with LSDIrecon ADC, i.e., always 250X smaller
  3. Including zeros (Steve's added button) did not make a difference. Does this mean 1) there is no difference, or 2) the "include zeros" button does not work?


Diffusion cases acquired Coronal AP (details here)

  • Fiber tracking seems to be fine on these cases


2 ROI method for DTI fiber tracking (details here)

  • I can't get it to work- please help!
  • "NOT" functionality: Raul is working on it


Higher resolution scans on 3T (details here)

  • Fibertracking was done after smoothing the tensor.


Fiber clustering (detailshere)

  • fiber backtracking/corpus labeling method?


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

  • Marek, do we know what variables/examples she wants from us?



Other issues...

  • Stephan's LSDIrecon code (details here)
  • Background noise in DTMRI scalar measures (details here)
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