dmipy
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AthenaEPI
The open source toolbox for reproducible diffusion MRI-based microstructure estimation
I get this warning from running "MultiCompartmentSphericalHarmonicsModel" function using solver='csd_cvxpy'. I checked the requirement of CVXPY 1.0.13 which is python 2. and dmipy requires python 3. should i ignore the...
Hi, I have recently set up an acquisition for collecting data amenable to Diffusion Basis Spectrum Imaging (DBSI) in a large hemorrhagic stroke dataset. It seems there are currently no...
Hi Rutger, I have encounterd errors while running NODDI_mod_watson.fit, Here is the error NODDI_fit_watson = NODDI_mod_watson.fit(gtab_dmipy, data, mask=mask) File "/home/yehp/anaconda3/lib/python3.7/site-packages/dmipy/core/modeling_framework.py", line 1201, in fit self, self.scheme, x0_, Ns, N_sphere_samples) File...
Hi @matteofrigo @rutgerfick We are trying to follow this example: (https://nbviewer.jupyter.org/github/AthenaEPI/dmipy/blob/master/examples/example_multi_compartment_spherical_mean_technique.ipynb) but in the multi-tissue framework: When trying to input the tissue responses we have tried with one tissue response:...
@matteofrigo @rutgerfick In your example for NODDI Watson (https://nbviewer.jupyter.org/github/AthenaEPI/dmipy/blob/master/examples/example_noddi_watson.ipynb) at the very end you explain that to get the ICVF you multiply the `partial_volume_1 * SD1WatsonDistributed_1_partial_volume_0` I am following your...
@rutgerfick We are trying to run a multi-tissue, multi-compartment SMT model, with the classic stick and zeppelin bundled together, and tortuosity and equality constraints included. We have precalculated a tissue...
Hi @matteofrigo @rutgerfick As mentioned before we are cascading a full ICVF map into a multi-tissue MCMDI 3 compartment model. We are inputting the tissue responses which are in the...
Hi @rutgerfick, Last we spoke we had discussed splitting up shells for calculations of various compartments. We have a dataset with _b=0,500,1000,2000_ and we were going to try and use...
Hi @matteofrigo @rutgerfick We have been trying to run MCMDI models on UKBB data and we were getting the following error: ``` File "/Users/jvillalo/opt/anaconda3/lib/python3.8/site-packages/dmipy/signal_models/cylinder_models.py", line 121, in spherical_mean E_mean[~acquisition_scheme.shell_b0_mask] =...