This is a collaborative space. In order to contribute, send an email to maximilien.chaumon@icm-institute.org
On any page, type the letter L on your keyboard to add a "Label" to the page, which will make search easier.
app-mean-transformation-matrix
- Aurore Bussalb (Unlicensed)
APP UNDeR development Private app on bl
This app aims at computing the mean transformation matrix across all runs of a MEG session to correct the head position of all runs thanks to this matrix. This mean transformation matrix is stored in an empty .fif file, which then can be passed as a parameter in mne.preprocessing.maxwell_filter (destination parameter).
GitHub repository
Brainlife datatype used:
For input: neuro/meg/fif
For output: neuro/meg/fif-override
Inputs of the App:
Files | Format | Datatype | Description | Optional |
|---|---|---|---|---|
MEG signal | .fif | meg/fif | first run | No |
MEG signal | .fif | meg/fif | second run | No |
… | … | … | … | Yes |
MEG signal | .fif | meg/fif | nth run | Yes |
At least two runs are required.
Output of the App:
Files | Format | Datatype | Description |
|---|---|---|---|
Raw file | .fif | meg/fif-override |
|
Besides, in the output directory, there are the optional files that can be used in a next App. This is mandatory, because the App that will be run after app-mean-transformation-matrix can take as input all the files in app-mean-transformation-matrix’s output directory corresponding to the datatype of the input of the next App (see How to run Apps one after another).
Parameters of the App
The parameters of the App correspond to the parameters passed to the Python functions used in the App. Their default values proposed in Brainlife or in config.json.example correspond to the default values of MNE Python 0.23.
Next improvements
Rename it into “app-compute-realigment-matrix”?
Allow the user to compute a destination.fif that is not the mean of all the runs but a specific run (this option is available is
mne-bids-pipeline. To do so, it would be best not to save the entire .fif file (i.e. the MEG signals) but to extract theraw.info[“dev_head_t"]["trans"]from this run and put it in an empty fif file, like we do when we compute the mean of the runs (it would save space).Make sure that it is okay to run this app after of before
app-head-pos, the order must not matter.