tissue electrical properties assignment

[jaystock]

It would be useful for RF coil simulations (and other applications) if conductivity and permittivity were assigned to each compartment. These parameters vary with frequency so we might want to make both a 3T and 7T version of the models, for starters. This could also be useful for other imaging modalities such as electrical impedance tomography. And it would be very useful for MRI RF coil Tx and Rx field simulations.

[evaalonsoortiz]

Great suggestion, we will add conductivity and permittivity values to our todo list! This is a good intern project.

[jcohenadad]

Just to cross-reference, related to discussion in this thread: shimming-toolbox/susceptibility-to-fieldmap-fft#6 (comment)

[evaalonsoortiz]

@sriosq @jaystock Are you aware of this resource: https://itis.swiss/virtual-population/regional-human-models/btpm-repository/ ?

[sriosq]

Hello @jaystock

As of commit a0e0f00 now, one can create Permittivity and Conductivity phantoms at 3T and 7T based on the dictionary of labels from the dataset: https://openneuro.org/datasets/ds005616/versions/1.1.2

To create the phantoms through the command line an example of the command is:

tissue_to_MR -i sub-amuAL_T1w_label-all.nii.gz -s compare_fm -v ds005616 -t perm3T -o amu_AL_perm3T.nii.gz

You can change perm3T for: perm7T, cond3T or cond7T and it will create the respective phantoms.

Please let me know if something isn't working as expected.
Thanks!

[mathieuboudreau]

@sriosq can you recap the slack conversation? What's the next steps / who's assigned to them

[jaystock]

Thank you for the update. Is there a plan to run the script for 7T and create permittivity and conductivity models for all 60 of the subjects and then upload this to the OpenNeuro archive? Could this be automated easily with a script?

[jcohenadad]

@sriosq could you please follow our usual procedures for code development and release workflow? Right now, when looking at the README, we see this:

it says v1.0, but my understanding is that now we have another version, right?

I suggest to automatize the generation of that table to avoid confusion: #23

[sriosq]

A quick recap of our conversation on slack: We would like to create Permittivity and Conductivity maps from available segmentations from last years whole-spine open neuro dataset. We need to add these properties to the tissue2MR repository. What's needed now is to run tissue2MR on all the subjects as the code to create the permittivity/conductivity phantoms is ready.

In terms of the creation of the maps, I'll be working on the script that will create the permittivity and conductivity maps for each subject which then will be updated to the Open Neuro archive.

@jcohenadad I will work on this to avoid errors in the future, will follow up on that issue - thank you!