Svs segment output details

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1

When I run “svs_segment -t T1.nii.gz -f tissue_frac svs_data.nii.gz” it prints tissue values like these,

“tissue1”: 531155,
“tissue2”: 640340,
“tissue3”: 610950,
“total_tissue”: 1.78245e+06

and at the end it outputs a json file,

{
“CSF”: 0.10685142694765949,
“GM”: 0.6841947892765805,
“WM”: 0.2089537837757599
}.

My first question is what is tissue1, tissue2, tissue3. Is it csf, gm, wm? I want to know what each of these tissue1, tissue2, tissue3 corresponds to.

And how are these csf : 0.1068, gm: 0.684 values calculated, because when I take ratio of tissue1/total_tissue. I don’t see any matches.

2

Hi @Dhruv_21 ,

I don’t recognise the first output

“tissue1”: 531155,
“tissue2”: 640340,
“tissue3”: 610950,
“total_tissue”: 1.78245e+06

as part of svs_segment (code here), so I think it’s some output from part of the fsl_anat script that calls various parts of fsl (e.g. bet, fast, etc.). I don’t have time to trawl through the other fsl source code to find the meaning of this, sorry. However, I would not assume that it has anything to do with the amount of each tissue in the MRS voxel (as the fsl_anat stage has no knowledge of the voxel).

The way the output values are calculated can be seen from this line. If you want to see the mask that is used see the mask.nii.gz output.

3

Thanks for the response,

From the code, it looks like tissue1, tissue2, tissue3 corresponds to csf, gm, wm tissue values in entire brain image.

Where can I find the fsl.wrappers folder?