Usage: @DiceMetric <-base BASE> <-dsets DSET1 [DSET2 ...]>
[max_N_roi MAX_ROI] [-keep_tmp]
Computes Dice Metric between BASE, and each of DSET volumes
Mandatory parameters:
<-base BASE>: Name of base (reference) segmentation
BASE is computed. This option is to be the last on the command line.
NOTE: A lazy usage would be: @DiceMetric BASE DSET
Optional parameters:
[-save_match] : Save volume showing BASE*equals(BASE,DSET)
- [-save_diff\ ] : Save volume showing BASE*(1-equals(BASE,DSET))
These two options are off by default. The output filenames are formed this way:
PATH_DSET/PREFIX_BASE.EQ.PREFIX_DSET PATH_DSET/PREFIX_BASE.DF.PREFIX_DSET
- [-max_N_roi MAX_ROI]: The maximum possible roi index. Default is 12
- or based on LTFILE if specified
- [-labeltable LTFILE]: If given, the labeltable is used to set the
- default MAX_ROI parameter Also, this option forces an output for each key in the LTFILE
[-forceoutput LTFILE]: If given force output for each class in LTFILE
- [-do_not_mask_by_base]: Do not mask dset by step(base) before computing
- Dice coefficient. This is the default behaviour for backward compatibility.
- [-mask_by_base]: Mask dset by the step(base) before computing
- Dice coefficient. With this option, Voxels that are 0 in the base dataset are not considered in the computations.
- [-prefix PREFIX]: Use PREFIX for the output table.
- Default is separate results for each dset to stdout
- [-ignore_bad]: Warn if encountering bad scenarios, but do not create
- a zero entry. You should check for the cause of the warnings to be sure they are OK to ignore
- [-keep_tmp]: Keep temporary files for debugging. Note that you should
- delete temporary files before rerunning the script.
[-echo] : set echo
Ziad Saad (saadz@mail.nih.gov) SSCC/NIMH/ National Institutes of Health, Bethesda Maryland