Add RIRO and Static masks to realtime zshimming

[po09i]

Description

With the goal of improving our realtime zshimming workflow, we can enhance our masking capability. We currently mask the shimming region we want to improve. Adding the ability to mask the riro component and the static component independently would be a nice feature and a lead to further investigations.

This PR adds nii_mask_anat_static and nii_mask_anat_riro to the realtime_zshim() API and appropriately masks the relevant components. The PR also adds mask_riro and mask_static options to the st_realtime_zshim CLI. The relevant tests were modified and the demo shell script was updated.

Linked issues

Fixes #220

[evaalonsoortiz]

I am trying to test this out an getting the following error:

The filename for the output mask is: /Users/evaalonsoortiz/Documents/Academic/Postdoc_Julien/Projects/Realtime_zShimming/Data/acdc_123p/rt_zshim_nifti/sub-example/fmap/sub-example_anat_mask.nii.gz
Usage: st_realtime_zshim [OPTIONS]
Try 'st_realtime_zshim -h' for help.

Error: no such option: -m

Note: I'm not using -m as an option in the call to st_realtime_zshim

[po09i]

Can you post the shell call you are using so I can try to reproduce the error

[evaalonsoortiz]

Can you post the shell call you are using so I can try to reproduce the error

st_prepare_fieldmap "sub-example_phasediff.nii.gz" -mag "sub-example_magnitude1.nii.gz" -unwrapper "prelude" -output "sub-example_fieldmap.nii.gz" -gaussian_filter=True || exit

st_mask box -input "../anat/sub-example_unshimmed_e1.nii.gz" -size 20 20 30 -center 60 32 7 -output "sub-example_anat_mask.nii.gz" || exit

st_realtime_zshim -fmap "sub-example_fieldmap.nii.gz" -anat "../anat/sub-example_unshimmed_e1.nii.gz" -resp "../../../realtime_zshimming_data/PMUresp_signal.resp" -mask_anat "sub-example_anat_mask.nii.gz" -mask_riro "sub-example_anat_mask.nii.gz" -output "." || exit

[jcohenadad]

@evaalonsoortiz no need for the "" in the syntax (quicker to type without them 😊 )

[po09i]

@evaalonsoortiz There was a typo in the shell script, the option was -mask_anat but it should have been -mask_static. I corrected it and it should work now.

[jcohenadad]

i didn't realize there was a mix of "-" and "_" in CLI flags. We should stick to "-" only-- can someone pls open an issue @charjl @po09i

[evaalonsoortiz]

@evaalonsoortiz There was a typo in the shell script, the option was -mask_anat but it should have been -mask_static. I corrected it and it should work now.

Just gave it another go, but still getting the same error ...

[po09i]

@evaalonsoortiz There was a typo in the shell script, the option was -mask_anat but it should have been -mask_static. I corrected it and it should work now.

Just gave it another go, but still getting the same error ...

Problem is now fixed. The error was the one described above here

[evaalonsoortiz]

Tested it out, looks good.