rkwitt/quicksilver

Predictive Image Registration

quicksilver's Issues

There are some problem in PyCA

Hello. I'm trying to run these codes, but I met some issue in PyCA.

(quicksilver) [hansoli@localhost applications]$ python qs_predict.py --moving-image ../CUMC_examples/m1.nii --target-image ../CUMC_examples/m2.nii --output-prefix /home/hansoli
Traceback (most recent call last):
  File "qs_predict.py", line 20, in <module>
    import PyCA.Core as ca
  File "/home/hansoli/anaconda3/envs/quicksilver/lib/python2.7/site-packages/PyCA/Core.py", line 28, in <module>
    _Core = swig_import_helper()
  File "/home/hansoli/anaconda3/envs/quicksilver/lib/python2.7/site-packages/PyCA/Core.py", line 24, in swig_import_helper
    _mod = imp.load_module('_Core', fp, pathname, description)
ImportError: /home/hansoli/quicksilver/3rd_party_software/pyca/Build/bin/libPyCA.so: undefined symbol: _ZN3itk27TransformFileReaderTemplateIdE16GetTransformListB5cxx11Ev

Anybody knows how to solve this? What version of package needed when compile PyCA?

I'm using machine with following environments:

Fedora 26
CUDA 8.0 (GTX 1050)
gcc 5.4 (for cuda), gcc 7.2 (for others)
swig 2.0.12 (i couldn't compile with latest 3.0.12)
InsightToolkit-devel 4.9.1
vxl-devel 1.17.0
fftw-devel 3.3.5
boost-devel 1.63.0
Python 2.7.13 (NumPy 1.13.1)

pyca - CMake Not Compiling

Hi, I am trying to compile pyca from the '3rd_party_software' directory, but failing to do so. I get the following errors:

CMake Warning (dev) at /usr/local/share/cmake-3.15/Modules/UseSWIG.cmake:607 (message):
  Policy CMP0078 is not set: UseSWIG generates standard target names.  Run
  "cmake --help-policy CMP0078" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

Call Stack (most recent call first):
  CMakeLists.txt:361 (SWIG_ADD_LIBRARY)
  Code/SWIG/CMakeLists.txt:37 (GEN_SWIG_MODULE)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/local/share/cmake-3.15/Modules/UseSWIG.cmake:460 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  /usr/local/share/cmake-3.15/Modules/UseSWIG.cmake:702 (SWIG_ADD_SOURCE_TO_MODULE)
  CMakeLists.txt:361 (SWIG_ADD_LIBRARY)
  Code/SWIG/CMakeLists.txt:37 (GEN_SWIG_MODULE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
CMake Error at CMakeLists.txt:372 (ADD_DEPENDENCIES):
  The dependency target "check_docstring" of target "_Core" does not exist.
Call Stack (most recent call first):
  Code/SWIG/CMakeLists.txt:37 (GEN_SWIG_MODULE)

Can you please help/suggest how to resolve this?

there is a error in the "code/vectormomentum/Code/Python/Libraries/CAvmCommon.py"

Cause the PyCA has changed its version, there is a error when using this code.

in the CAvmCommom, the function call “Splat(outMass, g, mass, False)” should be changed to "Splat(outMass, g, mass, 3, False)"

3 can be changed to 0~6 according to different situation

OASIS dataset link

I am trying to follow your example of how to retrain the network, but unfortunately cannot download the OASIS dataset in the format the yaml files ask for. Can you please add the link? (The instruction say "Download the OASIS dataset from TODO: add OASIS link here.")

Thank you

does this only support 2d image? Can it support 3d images with 2 different dimension?

about the icbm152

I am doing a research about multimodal image registration.I wonder how to use lddmm-shooting to achieve this(get the initial momentum)

Does it support Cross-modal image registration?

I am looking for Cross model image registration for some of my projects and I am wondering will it support cross-modal images.