Version: 4.11.0-2020-02-26
System: Mac
MR scanner: GE, 3.0T
Problem:
The components of the diffusion data can be checked successfully in Volume module and the FA map can be derived with Diffusion Tensor Estimation. The orientation of the map is marked correctly with anterior to posterior. But after running the whole brain fibers tractography with UKF method, the orientation changed into the directions (posterior to anterior) and contrary to the FA map. But if the data was loaded into Slicer using Dcm2niixGUI, the result was correct. What the reason about this and how to solve this problem?
the information after UKF tractography showed as below:
UKF Tractography standard output:
Using the 1T simple model. Setting the default parameters accordingly:
“*”: set by user
“-”: default setting
- stoppingFA: 0.06
- seedingThreshold: 0.1
- Qm: 0.005
- Ql: 300
- Rs: 0.01
- stepLength: 0.3
- recordLength: 0.9
- stoppingThreshold: 0.06
- seedsPerVoxel: 2
Found 12 cores on your system.
Running tractography with 12 thread(s).
Number of non-zero gradients: 25
Number of zero gradients: 1
Permuting the axis order to: 0 1 2 3
Resizing the data to: 25 256 256 39
Computing the baseline image
Dividing the signal by baseline image
Data normalization finished!
Using 1-tensor simple model.
Branching disabled
Using unconstrained filter
nmse_avg=0
vtkDebugLeaks has found no leaks.
UKF Tractography completed without errors
Very interesting, for another subject, after the diffusion data was loaded into Slicer with Dcm2niiGUI, the FA map looks normal but the fibers were in wrong direction again. If I handle the data with DTIPrep for motion and eddy current correction and load the data again, the fibers turned up down and only showed the superior part of the whole brain fibers.
The information of UKF Tractography showed as below:
UKF Tractography standard output:
Using the 1T simple model. Setting the default parameters accordingly:
“*”: set by user
“-”: default setting
- stoppingFA: 0.15
- seedingThreshold: 0.18
- Qm: 0.005
- Ql: 300
- Rs: 0.01
- stepLength: 0.3
- recordLength: 0.9
- stoppingThreshold: 0.1
- seedsPerVoxel: 2
Found 8 cores on your system.
Running tractography with 8 thread(s).
Number of non-zero gradients: 25
Number of zero gradients: 1
Permuting the axis order to: 0 1 2 3
Resizing the data to: 25 256 256 40
Computing the baseline image
Dividing the signal by baseline image
Data normalization finished!
Using 1-tensor simple model.
Branching disabled
Using unconstrained filter
nmse_avg=0
vtkDebugLeaks has found no leaks.