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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 registerd to SRI24 template. |
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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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| description | The required input for this stage is the tumor area in the raw image, can be prepared by using the raw image to multiply the tumor prediction label by stage 1. This command will give you the BraTS criteria's 3 class inner tumor segmentation label. == Install Instruction == |
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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 registerd to SRI24 template.
Example 2
mri_TumorSynth --i t1ce_tumor.nii.gz --o t1ce_tumor_mask.nii.gz --innertumor
The required input for this stage is the tumor area in the raw image, can be prepared by using the raw image to multiply the tumor prediction label by stage 1. This command will give you the BraTS criteria's 3 class inner tumor segmentation label.
Install Instruction
Bugs
None
See Also
Links
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>