python -m ipykernel install --user --name brainiak_36 --display-name "Brainiak 3.6"
Just an update @mihaic - so I deleted the environment and recreated from scratch. Got an MPI related error (as before):
(brainiak_36) DJW-2:brainIAK djw$ python3 -c "import brainiak.funcalign.srm" Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/djw/anaconda3/envs/brainiak_36/lib/python3.6/site-packages/brainiak/funcalign/srm.py", line 42, in <module> from mpi4py import MPI ImportError: dlopen(/Users/djw/anaconda3/envs/brainiak_36/lib/python3.6/site-packages/mpi4py/MPI.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libmpi.1.dylib Referenced from: /Users/djw/anaconda3/envs/brainiak_36/lib/python3.6/site-packages/mpi4py/MPI.cpython-36m-darwin.so Reason: image not found
Which was fixed by running:
brew install mpich
Then made the kernel accessible using
nb_conda instead of installing via
ipykernel and things worked.
Sorry if this isn't the right venue, but I have a question about brainiak searchlights :)
I have epi data in a .nii file, a full brain mask in a .nii file, as well as an array of TR labels in a .npy file. I'm trying to run a searchlight, and I get a message saying my searchlight object has no attribute 'blocks'. What does blocks refer to? I'm assuming its # of runs? I only have 1 run, but 4 different stimuli presented within that run. Is there a place I need to specify this?
Thanks so much for your help!
File "/jukebox/cohen/abby/fMRIMultitasking/BrainiakSearchlight/BrainiakTest.py", line 184, in <module>
sl_result = sl.run_searchlight(calc_svm, pool_size=pool_size)
File "/jukebox/pkgs/PYGER/neu350/lib/python3.6/site-packages/brainiak/searchlight/searchlight.py", line 470, in run_searchlight
File "/jukebox/pkgs/PYGER/neu350/lib/python3.6/site-packages/brainiak/searchlight/searchlight.py", line 398, in run_block_function
for idx, block in enumerate(self.blocks):
AttributeError: 'Searchlight' object has no attribute 'blocks'
macOS_SDK_headers_for_macOS_10.14.pkgas instructed) but am now getting a different error: in the fcma cython compilation I’m getting an error
brainiak/fcma/cython_blas.pyx:18:8: 'scipy/linalg/cython_blas.pxd' not found. This looks a lot like my environment is broken in some way but I’ve uninstalled/reinstalled scipy from both conda and pip and getting the same issue. I’ll try a totally fresh env but wondering if people have any other ideas.
condais cool if you set up your shell correctly for conda, I was in zsh without having it set up correctly)