[WIP] Adding b-tensor encoding scripts like compute_fodf/frf and metrics #425
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Hello @karanphil, Thank you for updating !
Comment last updated at 2022-06-30 14:32:43 UTC |
arnaudbore
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Here is the data. |
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Minor suggestions for @karanphil
All the CVX errors seem like warnings, the output is created and it looks fine.
| If you want to do DIVIDE with b-tensor data, you should use the following command. It will save files for the MD, uFA, OP, MK_I, MK_A and MK_T. This script should run in about 1-2 hours for a full brain. | ||
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| scil_compute_divide.py --in_dwis dwi_linear.nii.gz dwi_planar.nii.gz dwi_spherical.nii.gz --in_bvals dwi_linear.bval dwi_planar.bval dwi_spherical.bval --in_bvecs dwi_linear.bvec dwi_planar.bvec dwi_spherical.bvec --in_bdeltas 1 -0.5 0 --mask mask.nii.gz --fa fa.nii.gz --processes 8 -f |
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Can we also find a way to put this test data somewhere for people to try? Maybe a cropped version so it is light?
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I don't have the planar data, this example was very general.
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| if __name__ == "__main__": | ||
| main() |
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I'm getting this weird error when running on my mac:
(CVXPY) Mar 16 01:00:41 PM: Encountered unexpected exception importing solver SCS:
ImportError('dlopen(/Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/_scs_direct.cpython-310-darwin.so, 0x0002): Symbol not found: ___emutls_get_address\n Referenced from: <17C4D491-3B6D-344A-8328-189690282A3A> /Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/scs/.dylibs/libopenblasp-r0.3.21.dylib\n Expected in: /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib')
Is this a problem?
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I never got this error with Linux. This is weird. @arnaudbore what do you think? It looks like cvxpy tries to use some package that Max doesn't have.
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| if __name__ == "__main__": | ||
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Same error again.
(CVXPY) Mar 16 01:05:10 PM: Encountered unexpected exception importing solver SCS:
ImportError('dlopen(/Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/_scs_direct.cpython-310-darwin.so, 0x0002): Symbol not found: ___emutls_get_address\n Referenced from: <17C4D491-3B6D-344A-8328-189690282A3A> /Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/scs/.dylibs/libopenblasp-r0.3.21.dylib\n Expected in: /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib')
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/Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/cvxpy/problems/problem.py:1385: UserWarning: Solution may be inaccurate. Try another solver, adjusting the solver settings, or solve with verbose=True for more information.
warnings.warn(
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| if __name__ == "__main__": | ||
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(CVXPY) Mar 16 03:22:46 PM: Encountered unexpected exception importing solver SCS:
ImportError('dlopen(/Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/_scs_direct.cpython-310-darwin.so, 0x0002): Symbol not found: ___emutls_get_address\n Referenced from: <17C4D491-3B6D-344A-8328-189690282A3A> /Users/desm2239/my_env/scilpy_p10/lib/python3.10/site-packages/scs/.dylibs/libopenblasp-r0.3.21.dylib\n Expected in: /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib')
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Build passed ! Good Job 🍻 ! |
Here are three scripts
scil_compute_memsmt_frf.py,scil_compute_memsmt_fofd.pyandscil_compute_divide.pyenabling the use of tensor-valued dMRI data. The scripts are almost Scilpy ready, but the side modules are messy. This needs to be cleaned up before the PR is ready.