Hi there! Is there any sort of system in place for connecting people who are interested in sharing accommodations during the March workshop?
@danlurie Thinking out loud: may be creating a specific
dipy_workshop_accommodation channel in the
Mattermost workspace could help?
Hello, I'm not sure if this is the right place to ask. When using nipype, I found the c3d wrapper to be lacking in lots of different functions such as thresholding: https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.c3.html
Is there any way I can access all c3d functions from the nipype module? If not are there any plans to add this? Thank you!
from dipy.io.vtk import load_vtk_streamlinesdoesn't seem to be working. I don't see a utils vtk file under https://github.com/nipy/dipy/blob/master/dipy/viz/__init__.py. Is it possible to convert .vtk to .trk? Thanks! :)
Hi @skoudoro . I'm picking up after another researcher's project. Specifically, they used DIPY's symmetric diffeomorphic coregistration tool to extract a deformation map between two co-registered images. From what I understand, deformation maps tell how to "warp" features of one image to another registered image.
Extracting these deformation maps are very clear and easy (ie. get_forward_map). I currently have a set of deformation map and no longer have the latent data. It is not clear given the deformation map how I can warp an image to produce the registered image. Would you or someone else be able to comment/advise? Thank you!
Hi @b2jia, You need to create a
DiffeormorphicMap object and then apply the transformation to the desired image. it should be something like:
# Read your deformation map. I do not know how you save it. Then, create a object diff_map = imwarp.DiffeomorphicMap(3, domain_shape, domain_grid2world, domain_shape, domain_grid2world, codomain_shape, codomain_grid2world, None) # warp using linear interpolation warped = diff_map.transform(moving_image, 'linear')
But that is a good catch, we should update our Tutorial. Feel Free to create a PR and send us your small example for updating our Tutorial
@skoudoro Thank you so much! I'm happy to contribute to the community!
The diffeomorphic maps were saved as three separate images, corresponding (presumably) to translation along x, y, and z directions. I've written more extensively about my problem on GitHub, I will move my discussion there (hopefully it helps others as well!). Thanks for your response!