Difference between revisions of "Projects/Diffusion/Contrasting Tractography Measures/Slicer Tractography"

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{| align=center
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====Whole Brain Seeding====
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! Case !! Uncinate Fasciculus !! Internal Capsule !! Fornix !! Cingulum !! Arcuate Fasciculus
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Whole brain seeding followed by selection between two ROIs. Using eddy-corrected data set, without downsampling.
 +
 
 +
 
 +
Tensor estimation in DTMRI module in Slicer 2.8.
 +
The automatic brain mask generated in conversion step is used to prevent tracking in ventricles and outside the brain.
 +
 
 +
Tracts are seeded at a resolution of 2mm at points where cL > 0.3; tracking stops when cL drops below 0.15. Tracts shorter than 20mm are discarded. Remaining tracts are saved to disk as separate .vtk files.
 +
 
 +
====Tract selection====
 +
Using LaurenThesis module in Slicer 2.8, tracts are selected that pass through 2 specified ROIs.
 +
 
 +
For all cases of the arcuate fasciculus, none of the tracts generated were found to connect the two ROIs along the arcuate pathway.
 +
 
 +
====Measurement====
 +
For all cases, mean scalar measures (FA, mode, trace, linear, planar, spherical) were computed along each individual tract, then combined into a single average measure for each group of tracts. Measurements were done using a Matlab script.
 +
 
 +
For the cingulum, the three different groups of tracts for each side (L,R) were combined for a single mean measure (note that not all 3 groups were found for every case).
 +
 
 +
For the uncinate, internal capsule, and fornix, another matlab script was used to cut the tracts where they passed through the ROIs, so that the final measures included only the region of the tracts between the two ROIs. (The pictures below are positioned to show the regions measured; e.g., in the IC pictures, the tracts were measured between the two coronal slices which held the ROIs).
 +
 
 +
 
 +
 
 +
{|  
 +
! Case !! Uncinate Fasciculus !! Internal Capsule !! Fornix !! Cingulum (Left) !! Cingulum (Right)
 
|-
 
|-
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| caseD00917 || [[Image:CaseD00917_tracts_cut.png|thumb|150px]] || [[Image:917.png|thumb|150px]] || [[Image:917_fx.png|thumb|150px]] ||
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| caseD00917 || [[Image:CaseD00917_tracts_cut.png|thumb|150px]] || [[Image:917.png|thumb|150px]] || [[Image:917_fx.png|thumb|150px]] || [[Image:917_cing_L.png|thumb|150px]] || [[Image:917_cing_R.png|thumb|150px]]
 
|-
 
|-
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| caseD00920 || [[Image:CaseD00920_tracts_cut.png|thumb|150px]] || [[Image:920.png|thumb|150px]] || [[Image:920_fx.png|thumb|150px]] ||
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| caseD00920 || [[Image:CaseD00920_tracts_cut.png|thumb|150px]] || [[Image:920.png|thumb|150px]] || [[Image:920_fx.png|thumb|150px]] || [[Image:920_cing_L.png|thumb|150px]] || [[Image:920_cing_R.png|thumb|150px]]
 
|-
 
|-
−
| caseD00924 || [[Image:CaseD00924_tracts_cut.png|thumb|150px]] || [[Image:924.png|thumb|150px]] || [[Image:924_fx.png|thumb|150px]] ||  
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| caseD00924 || [[Image:CaseD00924_tracts_cut.png|thumb|150px]] || [[Image:924.png|thumb|150px]] || [[Image:924_fx.png|thumb|150px]] || [[Image:924_cing_L.png|thumb|150px]] || [[Image:924_cing_R.png|thumb|150px]]
 
|-
 
|-
−
| caseD00925 || [[Image:CaseD00925_tracts_cut.png|thumb|150px]] || [[Image:925.png|thumb|150px]] || No tracts selected ||  
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| caseD00925 || [[Image:CaseD00925_tracts_cut.png|thumb|150px]] || [[Image:925.png|thumb|150px]] || <center>No tracts selected</center> || [[Image:925_cing_L.png|thumb|150px]] || [[Image:925_cing_R.png|thumb|150px]]
 
|-
 
|-
−
| caseD00928 || [[Image:CaseD00928_tracts_cut.png|thumb|150px]] || [[Image:928.png|thumb|150px]] || [[Image:928_fx.png|thumb|150px]] ||
+
| caseD00928 || [[Image:CaseD00928_tracts_cut.png|thumb|150px]] || [[Image:928.png|thumb|150px]] || [[Image:928_fx.png|thumb|150px]] || [[Image:928_cing_L.png|thumb|150px]] || [[Image:928_cing_R.png|thumb|150px]]
 
|-  
 
|-  
−
| caseD00935 || [[Image:CaseD00935_tracts_cut.png|thumb|150px]] || [[Image:935.png|thumb|150px]] || [[Image:935_fx.png|thumb|150px]] ||  
+
| caseD00935 || [[Image:CaseD00935_tracts_cut.png|thumb|150px]] || [[Image:935.png|thumb|150px]] || [[Image:935_fx.png|thumb|150px]] || [[Image:935_cing_L.png|thumb|150px]] || [[Image:935_cing_R.png|thumb|150px]]
 
|-
 
|-
−
| caseD00936 || [[Image:CaseD00936_tracts_cut.png|thumb|150px]] || [[Image:936.png|thumb|150px]] || [[Image:936_fx.png|thumb|150px]] ||  
+
| caseD00936 || [[Image:CaseD00936_tracts_cut.png|thumb|150px]] || [[Image:936.png|thumb|150px]] || <center>No tracts selected</center> || [[Image:936_cing_L.png|thumb|150px]] || [[Image:936_cing_R.png|thumb|150px]]
 
|-  
 
|-  
−
| caseD00938 || [[Image:CaseD00938_tracts_cut.png|thumb|150px]] || [[Image:938.png|thumb|150px]] || [[Image:938_fx.png|thumb|150px]] ||
+
| caseD00938 || [[Image:CaseD00938_tracts_cut.png|thumb|150px]] || [[Image:938.png|thumb|150px]] || [[Image:938_fx.png|thumb|150px]] || [[Image:938_cing_L.png|thumb|150px]] || [[Image:938_cing_R.png|thumb|150px]]
 
|-  
 
|-  
−
| caseD00939 || [[Image:CaseD00939_tracts_cut.png|thumb|150px]] || [[Image:939.png|thumb|150px]] || [[Image:939_fx.png|thumb|150px]] ||
+
| caseD00939 || [[Image:CaseD00939_tracts_cut.png|thumb|150px]] || [[Image:939.png|thumb|150px]] || [[Image:939_fx.png|thumb|150px]] || [[Image:939_cing_L.png|thumb|150px]] || [[Image:939_cing_R.png|thumb|150px]]
 
|-
 
|-
−
| caseD00940 || [[Image:CaseD00940_tracts_cut.png|thumb|150px]] || [[Image:940.png|thumb|150px]] || [[Image:940_fx.png|thumb|150px]] ||
+
| caseD00940 || [[Image:CaseD00940_tracts_cut.png|thumb|150px]] || [[Image:940.png|thumb|150px]] || [[Image:940_fx.png|thumb|150px]] || [[Image:940_cing_L.png|thumb|150px]] || [[Image:940_cing_R.png|thumb|150px]]
 
|}
 
|}
 +
 +
 +
====Results====

Latest revision as of 18:43, 26 September 2007

Home < Projects < Diffusion < Contrasting Tractography Measures < Slicer Tractography

Whole Brain Seeding

Whole brain seeding followed by selection between two ROIs. Using eddy-corrected data set, without downsampling.


Tensor estimation in DTMRI module in Slicer 2.8. The automatic brain mask generated in conversion step is used to prevent tracking in ventricles and outside the brain.

Tracts are seeded at a resolution of 2mm at points where cL > 0.3; tracking stops when cL drops below 0.15. Tracts shorter than 20mm are discarded. Remaining tracts are saved to disk as separate .vtk files.

Tract selection

Using LaurenThesis module in Slicer 2.8, tracts are selected that pass through 2 specified ROIs.

For all cases of the arcuate fasciculus, none of the tracts generated were found to connect the two ROIs along the arcuate pathway.

Measurement

For all cases, mean scalar measures (FA, mode, trace, linear, planar, spherical) were computed along each individual tract, then combined into a single average measure for each group of tracts. Measurements were done using a Matlab script.

For the cingulum, the three different groups of tracts for each side (L,R) were combined for a single mean measure (note that not all 3 groups were found for every case).

For the uncinate, internal capsule, and fornix, another matlab script was used to cut the tracts where they passed through the ROIs, so that the final measures included only the region of the tracts between the two ROIs. (The pictures below are positioned to show the regions measured; e.g., in the IC pictures, the tracts were measured between the two coronal slices which held the ROIs).


Case Uncinate Fasciculus Internal Capsule Fornix Cingulum (Left) Cingulum (Right)
caseD00917
CaseD00917 tracts cut.png
917.png
917 fx.png
917 cing L.png
917 cing R.png
caseD00920
CaseD00920 tracts cut.png
920.png
920 fx.png
920 cing L.png
920 cing R.png
caseD00924
CaseD00924 tracts cut.png
924.png
924 fx.png
924 cing L.png
924 cing R.png
caseD00925
CaseD00925 tracts cut.png
925.png
No tracts selected
925 cing L.png
925 cing R.png
caseD00928
CaseD00928 tracts cut.png
928.png
928 fx.png
928 cing L.png
928 cing R.png
caseD00935
CaseD00935 tracts cut.png
935.png
935 fx.png
935 cing L.png
935 cing R.png
caseD00936
CaseD00936 tracts cut.png
936.png
No tracts selected
936 cing L.png
936 cing R.png
caseD00938
CaseD00938 tracts cut.png
938.png
938 fx.png
938 cing L.png
938 cing R.png
caseD00939
CaseD00939 tracts cut.png
939.png
939 fx.png
939 cing L.png
939 cing R.png
caseD00940
CaseD00940 tracts cut.png
940.png
940 fx.png
940 cing L.png
940 cing R.png


Results

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