The shape of the T1 image and the shape of the electric field are different

[lucky_lin]

I used the IXI025-Guys-0852-T1 image for head segmentation and then performed TI (tissue imaging) simulation. However, I found that the shape of the T1 image and the shape of the electric field are different. My simulation grid setting is 1 mm. Why is this the case?

[lucky_lin]

I tried to change the grid size but still couldn't make it exactly the same as the T1 image. I wonder if it's possible to control the electric field slices to be exactly the same as the T1 image.

[bryn]

You don't have the same resolution (grid spacing) in the T1 image and the efield...!
To visualize the two "fields" on the same grid, drag the T1w image to the analysis explorer, and interpolate it on the e-field grid.

The interpolator has two inputs:

1. T1w image (input field)
2. E-field (target grid)

Here is a snippet to show this could be done in Python

import s4l_v1.analysis as analysis
import s4l_v1.document as document
import s4l_v1.model as model

# Add a new ModelToGridFilter
inputs = []
model_to_grid_filter = analysis.core.ModelToGridFilter(inputs=inputs)
model_to_grid_filter.Name = "Image"
model_to_grid_filter.Entity = model.AllEntities()["T1w-image"]  # The model entity corresponding to the T1w-image
model_to_grid_filter.UpdateAttributes()

# Add a new SimulationExtractor
simulation = document.AllSimulations["EM"]
simulation_extractor = simulation.Results()

# Add a new EmSensorExtractor
em_sensor_extractor = simulation_extractor["Overall Field"]
em_sensor_extractor.FrequencySettings.ExtractedFrequency = u"All"

# Add a new FieldInterpolationFilter
inputs = [model_to_grid_filter.Outputs[""], em_sensor_extractor.Outputs["EM E(x,y,z,f0)"]]
field_interpolation_filter = analysis.core.FieldInterpolationFilter(inputs=inputs)
field_interpolation_filter.UpdateAttributes()
document.AllAlgorithms.Add(field_interpolation_filter)

Then you will have the same grid and array ordering, and can overlay the T1w image and the field (or display them side by side with identical aspect ratio).

Note if your simulation grid is not uniform, matplotlib will depict the anatomy in a distorted way.
Btw, you could also interpolate in the other direction ...

[lucky_lin]

@bryn Can I export the new T1.nii.gz file? The T1 and the electric field seem to be in opposite directions along the x-axis. If I can export it, will the new T1 have the same orientation as the original one?