<> = 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 = See Also = [[othercommand1]], [[othercommand2]] = Links = FreeSurfer, FsFast = References = [[References/Wu###]] = Reporting Bugs = Report bugs to = Author/s = JaneSmith