Coder Social home page Coder Social logo

eigenstrapping's People

Contributors

nikitas-k avatar sng-newy avatar vincebaz avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar

eigenstrapping's Issues

Problem with dependencies

Hi,
thanks for providing this extensive package! I did pip install the python dependencies using the provided requirements.txt, followed by pip installing eigenstrapping. Everything went smoothly but I then got an error while import geometry from eigenstrapping:
ImportError: cannot import name '_stats' from 'scipy.ndimage.measurements' (/Library/Frameworks/Python.framework/V ersions/3.9/lib/python3.9/site-packages/scipy/ndimage/measurements.py)
What's the issue here? Scipy was successfully installed...

SurfaceEigenstrapping str or array

Hi,

Thanks for this awesome tool. I'm following Tutorial 3 to generate my own surrogate maps and I can't determine whether SurfaceEigenstrapping requires an array or a string:

AttributeError                            Traceback (most recent call last)
Input In [82], in <module>
      1 from eigenstrapping import SurfaceEigenstrapping
----> 2 t = SurfaceEigenstrapping(surface='../tpl-avg_space-canonical_den-1mm_label-hipp_midthickness.surf.gii'
      3                               ,data='../thickness_midsurf_L_mean.shape.gii', num_modes=200)

File /export03/data/opt/venv/lib/python3.8/site-packages/eigenstrapping/base.py:329, in SurfaceEigenstrapping.__init__(self, data, surface, evals, emodes, num_modes, save_surface, seed, decomp_method, medial, randomize, resample, n_jobs, use_cholmod, permute, add_res, save_rotations, parcellation, normalize)
    326     self.surface = load_surface(self.surface_file)
    328 self.data = copy.deepcopy(data)
--> 329 self.n_vertices = self.data.shape[0]
    331 if emodes is not None and evals is not None:
    332     self.evals = evals[:num_modes]

AttributeError: 'str' object has no attribute 'shape'

input files here:
https://github.com/MICA-MNI/hippomaps/blob/master/resources/canonical_surfs/tpl-avg_space-canonical_den-1mm_label-hipp_midthickness.surf.gii
https://github.com/MICA-MNI/hippomaps/blob/master/hippomaps/example_data/thickness_midsurf_L_mean.shape.gii

Thanks!

making sense of the method

Hi!

I was following the tutorial and created SurfaceEigenstrapping class with my data. When I am plotting the eigen.reconstructed_data it looks much smoother than my original data. Moreover, residuals seem to carry some information. I am using 1000 eigenmodes. Should it be like this? Could you advise what I need to change?

Here is my code

src = mne.setup_source_space(subject, spacing='oct6', subjects_dir=subjects_dir, add_dist=False, n_jobs=10)
vox16_to_vox8 = {ivox:i for i, ivox in enumerate(src[0]['vertno'])}
used_tris_dsmp = [[vox16_to_vox8[tri[0]], vox16_to_vox8[tri[1]], vox16_to_vox8[tri[2]]] for tri in src[0]['use_tris']]
surface=(src[0]['rr'][src[0]['inuse'].astype(bool)].T, used_tris_dsmp)
tria = TriaMesh(surface[0], surface[1])
evals, emodes = calc_eig(tria, 1000, False)

eigen = SurfaceEigenstrapping(
    emodes=emodes,
    evals=evals,
    data=data[:4098],
    num_modes=1000,
    save_rotations=True,
    normalize=False
)

[BUG][LOW] Python kernel panic when reinstalling eigenstrapping from git

Priority: Low

Replicable by developers: No

Users involved: One

User has Python kernel panic when importing eigenstrapping libraries into jupyter notebook. Reinstalling package from local git install caused the issue.

Developer cannot reproduce issue on multiple devices and fresh environments. Suggest this is a one-off error related to user's system.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.