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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] I will try to change this |
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###]] |
Contents
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. |
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--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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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
See Also
Links
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>