Operating system: Mac OSX 10.9.5
Slicer version: 4.7
I am trying to run a registration in the BRAINS module, that is somewhat unique and different from the sample cases given online. I have a grayscale FA scalar volume image file (obtained from a DTI volume file), and I have generated an FEM mask of the actual brain section used, by means of a Matlab code. The FEM mask consists of 80-odd slices, and the file format is NifTI. I followed the protocol for BRAINS general reg. per the tutorial for DTI registration on the Slicer forum. The steps I followed and the parameters I used are as follows:
Load the FAV1 file.
Load the FEM masks. I loaded this as a directory, since I have 80 individual slices which I can load in 3D slicer in a way that I can scroll through them as a volume file. They start with slice # slice001, and go upwards in number. [Note: in the option bar where the foreground and background can be selected, only slice001 shows up, but I can still scroll through all 80 slices]
I then chose to keep the FAV1 file as my foreground at 0.5 opacity, and the FEM mask directory, slice001, as my background. [Note: Changing the visibility of the files does not help at all. I am able to only see the file I load last, whichever it may be].
I opened the Gen. reg. BRAINS module, and set the parameters like this. Basically, I did not alter anything except the fixed and moving image inputs. All other default numerical parameters were the same. I used the B-spline method.
The registration completes with errors (and barely takes a second or 2 to complete). The error is as follows:
General Registration (BRAINS) standard error:
WARNING: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/ITKv4/Modules/Numerics/Optimizersv4/src/itkLBFGSBOptimizerv4.cxx, line 116
LBFGSBOptimizerv4 (0x104b0e210): LBFGSB optimizer does not support scaling. All scales are set to one.
libc++abi.dylib: terminating with uncaught exception of type itk::ExceptionObject: /Users/kitware/Dashboards/Nightly/Slicer-0-build/BRAINSTools/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx:1552:
_itk::ERROR: Exception caught: _
_Location: “unknown” _
Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x104b02930): Joint PDF summed to zero
General Registration (BRAINS) standard output:
Original Fixed image origin[0, 0, 0, 0]
TranformTypes: BSpline(1 of 1).
=============================== ITKv4 Registration: Starting Transform Estimations for BSpline(1 of 1).===============================
Initialized BSpline transform is set to be an identity transform.
_ - Number of parameters = 9945_
– WARNING: Only one in every 663 parameters is printed on screen.
_ - Cost Function Convergence Factor : 2e+13_
_ - Projected Gradient Tolerance : 1e-05_
_ - Maximum Number of Corrections : 25_
_ - Maximum Number of Evaluations : 900_
_ - Maximum Number of Iterations : 1500_
*** Running bspline registration (meshSizeAtBaseLevel = [14, 10, 12]) ***
After this point, I really don’t know what else I can do. I have tried different combinations of file loading, but nothing seems to work. I even centered the 2 files to the same origin, but I was still unable to view them together. I would be happy to provide the files if need be.
Sorry for the long post, but I would really like some insight into fixing this issue! Thank you in advance!