Differences

This shows you the differences between two versions of the page.

--- jvs:fscan:manual:chapter2:roistats [2023/10/18 17:44] – [-roi stats] voyvodic
+++ jvs:fscan:manual:chapter2:roistats [2023/10/18 18:10] – [-roi stats] voyvodic
@@ Line 4: / Line 4: @@
   * -roi MEAN flag
   * -roi CORREL flag refROI binsize corrROI name thresh
-  * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel
+  * -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] thresh nlevels level0 dlevel
+  * -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] thresh offroi ignoreroi onroi nlvls lvl0 dlvl
+  * -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] cycleleng cycle0 thresh
 ==== -roi stats====
@@ Line 28: / Line 30: @@
   * 02000 - calculate cycle-to-cycle variations (not with 010000 option)
   * 04000 - binary mask; values above threshold are ON (default if no REFIMAGE)
-  * 010000 - threshhold curves; calculate stats for 10 different threshold values
+  * 010000 - threshhold curves; calculate stats for 10 different threshold values (see THRESHOLD note)
-THRESH arg is the lowest threshold and stepsize.
+  * 020000 - include negative values
+  * 040000 - show only non-zero values, not total voxel counts
+  * 1000000 - use threshold, even if THRESH is 0 (this is default if THRESH is non-zero)
+THRESHOLD: THRESH arg is the lowest threshold and stepsize.
 If OFFROI is non-zero this will generate ROC curves.
 If IGNOREROI is non-zero, REFIMAGE voxels with that value are ignored.
 If ONROI is non-zero, only REFIMAGE voxels with that value are included.
-  * 020000 - include negative values
-  * 040000 - show only non-zero values, not total voxel counts
-  * 1000000 - threshold (?)
 SHOWFLAG - Report generation flags
   * 1 - tab-separated columns in text output (default is space-separated)
@@ Line 61: / Line 64: @@
   * 4 - atlas areas
   * 8 - threshold (can combine with 1-4)
-  *
 NAME - save stats in file NAME, if specified
-VAL: If VAL > 0, only calculate for this mask value
+MASKVAL: If > 0, only calculate for this mask value //
+PREFIX: string prepended to each data line in report \
+PRFXHDR: string prepended to column header lines in report \\
+THRESH: explicit threshold level (default is current image threshold, or if FLAG&010000 default is 0.5)
+OFFROI: if FLAG&010000, OFFROI is ROI value indicating true-negative voxels
+IGNOREROI: if FLAG&010000, ROI value to ignore when making ROC curves
+ONROI: if FLAG&010000, ROI value indicating true-positive voxels for ROC curves
+NLVLS: Number threshold levels to calculate separately (default=1, or 10 if FLAG&010000)
-NLVLS: Number threshold levels to calculate separately (default=1)
+Note: If you want a PREFIX without specifying output file NAME you must include a MASKVAL (0 for default) to avoid syntax confusion.
 If input is a Surface:\\