mri_TumorSynth

mri_TumorSynth - To segment the healthy brain tissue and tumor in MR scans with tumor.

Synopsis

mri_TumorSynth --i inputvol --o outputvol [--flag arg]

Arguments

Required Flagged Arguments

--i inputvol	input volume	Input data.
--o outputvol	save output	Save output after smoothing.

Optional Flagged Arguments

--wholetumor	Output brain tissue and whole tumor mask, Input format for this flag must be skull-striped and registered into SRI-24 templates.
--innertumor	Save output of inner tumor structures, outputting Tumor Core, Non-Enhancing Tumor, Odema classes. Input format for this flag must be tumor ROI image, Alternately, one can use the tumor mask outputted by --wholetumor flag and multiply raw image to get the tumor ROI image.

Description

description

Examples

Example 1

mri_TumorSynth --i t1ce.nii.gz --o t1ce_mask.nii.gz --wholetumor

This will give you the mask of the normal brain tissue and whole tumor mask, which include oedema, enhancing tumor and non-enhancing tumor. This t1ce is skull-striped and

Example 2

mri_TumorSynth --i t1ce_tumor.nii.gz --o t1ce_tumor_mask.nii.gz --innertumor

description

Bugs

None

Links

FreeSurfer, FsFast

References

References/Wu###

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

JaneSmith

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-= Name =

command - 1/2 sentence summary
+= mri_TumorSynth =

mri_TumorSynth - To segment the healthy brain tissue and tumor in MR scans with tumor.
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-command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]
+mri_TumorSynth --i inputvol --o outputvol [--flag arg]
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-== Positional Arguments ==

|| argA || brief description || detailed description (eg, help file information)  ||

|| argB || brief description || detailed description (eg, help file information)  ||
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-|| -flag1 arg1 || brief description || detailed description (eg, help file information) ||

|| -flag2 arg2 || brief description || detailed description (eg, help file information) ||
+||--i inputvol ||input volume ||Input data. ||

||--o outputvol ||save output ||Save output after smoothing. ||
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-|| -flag3 arg3 || brief description ||detailed description (eg, help file information) ||

|| -flag4 arg4 || brief description ||detailed description (eg, help file information) ||
+||--wholetumor ||Output brain tissue and whole tumor mask, Input format for this flag must be skull-striped and registered into SRI-24 templates.|| ||

||--innertumor ||Save output of inner tumor structures, outputting Tumor Core, Non-Enhancing Tumor, Odema classes. Input format for this flag must be tumor ROI image, Alternately, one can use the tumor mask outputted by --wholetumor flag and multiply raw image to get the tumor ROI image. || ||
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-= Outputs =

|| volume1 || description ||

|| volume2 || description ||
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-command foo -i f -o out
+mri_TumorSynth --i t1ce.nii.gz --o t1ce_mask.nii.gz --wholetumor
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-description
+This will give you the mask of the normal brain tissue and whole tumor mask, which include oedema, enhancing tumor and non-enhancing tumor. This t1ce is skull-striped and
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-command foo -i f -o out -f fvalue
+mri_TumorSynth --i t1ce_tumor.nii.gz --o t1ce_tumor_mask.nii.gz --innertumor
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-= Methods Description =

{{{

description

description

}}}
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-[[References/Lastname###]]
+[[References/Wu###]]