<> = 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 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. = Bugs = None = See Also = [[othercommand1]], [[othercommand2]] = Links = FreeSurfer, FsFast = References = [[References/Wu###]] = Reporting Bugs = Report bugs to = Author/s = JaneSmith