kousu
commented
4 years ago I've drawn up my current understanding of where this fits in. The overall goal is to tune an MRI to get better resolution(?)/accuracy(?)/variance(?) in the images taken.
At the high level, first, a calibration scan is done and some tunings computed (per-subject!/per-session!), then those tunings are fed into the real experimental/clinical scan.
In the details, there are several different kinds of images we can take (2d slices, 3d, 3d video, maybe 2d-slice-video?), different tuning methods ("pulse sequence programming" or shim coils -- and different models of coils at that), and different kinds of scanners (though we've agreed to only treat with a specific Siemens model for the MVP).
This leaves out a lot of pieces, some features (e.g. video mode?) and has gaps where my understanding falls short.
Here's the code, full of plenty of ugly but functional typos:
flowchart TD
subgraph Realtime Shimming
calib1-->calib2-->calib3
subgraph Calibration
subgraph calib1[Record MR images]
1_a[Welcome subject to lab]-->
1_b[Place subject in MRI scanner]
-->1_c[Wait for subject to settle]
-->1_d
subgraph 1_d[Acquire images]
1_d_1{Scan type}
1_d_1-->|3d| cjdhis[Acquire 3d image]
1_d_1-->|3d| diofjsdofj[Acquire 2d slices]
end
1_d-->1_e[Export .dcm fies from MRI machine to processing computer]
end
subgraph calib2[Compute magnetic field map]
calib2_a[Load .dcm images]
-->calibr_b[Construct complex-valued images by concatenating magnitiude+phase]
-->calib2_c[Unwrap phase distortions]
-->dsfds[Compute fieldmap]
-->casdfsfds[Output fieldmap]
end
subgraph calib3[Generate calibration data]
calib3_0[Compensation Methods]
calib3_0 --> calib3_a
calib3_0 --> calib3_c
calib3_a{Pulse-Sequence?}--Yes-->b[Output pulse-sequence config file for Eva's code]
calib3_c{Noise-cancelling coil?}--Yes-->d[Optimize shim coefficients]-->e[Output coil calibration coefficients]
end
end
subgraph Scanning
s0[Place subject in MRI scanner]
s0-->s1
subgraph s1[Set up Compensation Methods]
s11{Pulse-sequence?}
-->|Yes| s111[Upload pulse-sequence config file to MRI interface computer]
--> s112[Command MRI to download pulse-sequence config file]
s12{Noise-cancelling coil?}
-->|Yes| s121[Place coil near subject]
--> s122[Connect arduino control mechanism to coil]
--> s123[Connect computer to arduino]
--> s124[Start serial port daemon process]
--> s125[Load optimized coil coefficients into coil controller]
end
s1-->s2
subgraph s2[Acquire images]
s21{Scan type}
s21-->|3d| s211[Acquire 3d image]
s21-->|2d| s212[Acquire 2d slices]
end
s2-->s3
subgraph s3[Apply compensation]
isduhfisu[????]
end
s3-->s4[Display images]
end
Calibration -- Calibration data --> Scanning
endYou can edit this diagram here to make it more accurate.
Editorializing: I did this in mermaid and the result is pretty nice and I like where they're going with it but after working with it for a couple hours I think I would rather just use graphviz. Mermaid still has lots of quirks and bugs to iron out, and it's pretty slow to work with because its only implementation must run through javascript in a web browser. Visio or Inkscape are good GUI alternatives (Inkscape is especially nice in that it works on .svgs, in fact it is the defacto world svg editor, the same format Mermaid generates).
evaalonsoortiz
po09i
jcohenadad
gaspardcereza
As we are refactoring shimming-toolbox, it would be helpful to have an overview of the different processes and how they relate to each other. Notably, knowing the inputs/outputs will help us in the refactoring task.
This (or these) flowcharts should ideally cover all the possible scenario that we would like shimming-toolbox to cover.
Here is a link to the flowchart (click "open with diagrams.net", only editable for members of shimming-toolbox googlegroup): https://drive.google.com/file/d/1BqYuqOvTUyPTHhb3z19rktEv6lZU3ehM/view?usp=sharing