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Consider quantifying the ratio cord/CSF signal #63

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jcohenadad opened this issue Jan 17, 2024 · 4 comments · Fixed by #64
Closed

Consider quantifying the ratio cord/CSF signal #63

jcohenadad opened this issue Jan 17, 2024 · 4 comments · Fixed by #64

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@jcohenadad
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One problem with the current analysis pipeline, is the extraction of the magnitude signal on the T1w or T2starw images. The magnitude being also affected by receive coil sensitivity, it is hard to judge about the specific benefits of RF shimming.

One workaround would be to quantify and display and ratio of CSF/cord signal.
@jcohenadad
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Segmentation of the CSF with propseg is so-so:

anim

Consider adding thresholding on the CSF mask

@jcohenadad
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I did a quick quantification of cord/CSF ratio using the automated masks, for CoV and CP modes. I don't see striking differences:

image

@jcohenadad
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jcohenadad commented Jan 17, 2024 •
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Trying with another mask, created using dilation:

sct_maths -i sub-01_acq-CoV_T1w_crop_seg.nii.gz -dilate 3 -shape disk -dim 2 -o sub-01_acq-CoV_T1w_crop_seg_dil.nii.gz
sct_maths -i sub-01_acq-CoV_T1w_crop_seg_dil.nii.gz -sub sub-01_acq-CoV_T1w_crop_seg.nii.gz -o sub-01_acq-CoV_T1w_crop_seg_CSFdil.nii.gz
image

However, this did not help getting a more convincing discrepancy between the two shim modes:

image

@jcohenadad
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jcohenadad commented Jan 17, 2024 •
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The T2starw scan is more convincing though:

image

And if looking at the signal only in the cord, we do see the influence of the B1- field:

image

@jcohenadad jcohenadad mentioned this issue Jan 17, 2024
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jcohenadad added a commit that referenced this issue Jan 17, 2024
@jcohenadad
Compute cord/CSF ratio and removing T1w bloc (#64)
5055081 
Fixes Consider quantifying the ratio cord/CSF signal #63

* Removed T1w block

* Put back vertebral labeling on the T2starw scan

* Cosmetic changes

* Removed temp fix

* Create CSF mask

* Extract signal in T2starw scan in SC and CSF

* Display curves (WIP)

* Create curves (only for CoV and CP)

* Updated intro
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Compute cord/CSF ratio and removing T1w bloc shimming-toolbox/rf-shimming-7t
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@jcohenadad