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jvs:fscan:manual:chapter2:roistats
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| Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
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jvs:fscan:manual:chapter2:roistats [2018/03/14 16:23] voyvodic |
jvs:fscan:manual:chapter2:roistats [2023/10/18 18:11] voyvodic [-roi stats] |
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| Line 4: | Line 4: | ||
| * -roi MEAN flag | * -roi MEAN flag | ||
| * -roi CORREL flag refROI binsize corrROI name thresh | * -roi CORREL flag refROI binsize corrROI name thresh | ||
| - | * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | + | * -roi STATS refimage flag showflag |
| + | * -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==== | ==== -roi stats==== | ||
| Line 24: | Line 26: | ||
| * 0100 - report ROI volumes in mm3 (voxel count X voxel volume) | * 0100 - report ROI volumes in mm3 (voxel count X voxel volume) | ||
| * 0200 - include ROI's with only zero values (usually ignored) | * 0200 - include ROI's with only zero values (usually ignored) | ||
| + | * 0400 - weight average by overlay map values | ||
| + | * 01000 - ignore thresholds (default: use threshold if active) | ||
| + | * 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 (see THRESHOLD note) | ||
| + | * 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. | ||
| SHOWFLAG - Report generation flags | SHOWFLAG - Report generation flags | ||
| * 1 - tab-separated columns in text output (default is space-separated) | * 1 - tab-separated columns in text output (default is space-separated) | ||
| * 2 - comma-separated columns in text output | * 2 - comma-separated columns in text output | ||
| + | * 3 - use space as separator | ||
| * 4 - do not write out stats (no stats file) | * 4 - do not write out stats (no stats file) | ||
| + | * 020 - include ROIs with 0 values in report | ||
| * 0100 - save as XML text file | * 0100 - save as XML text file | ||
| * 0200 - save as non-XML text file | * 0200 - save as non-XML text file | ||
| + | * 0300 - print in table format; lines identified by prefix | ||
| * 0400 - plot ref time series | * 0400 - plot ref time series | ||
| * 01000 - save as ref time series | * 01000 - save as ref time series | ||
| * 02000 - generate AMPLE statistics | * 02000 - generate AMPLE statistics | ||
| - | * 04000 - ignore thresholds | + | * 04000 - print stats to 4 decimal points |
| - | * 010000 - Watch flag (?) | + | * 010000 - show XYZ locs in ROOM coordinates) |
| + | * 020000 - show XYZ locs in Talairach coords | ||
| + | * 040000 - put format ID on each line | ||
| + | * 0100000 - no output | ||
| | | ||
| MODE | MODE | ||
| Line 44: | Line 64: | ||
| * 4 - atlas areas | * 4 - atlas areas | ||
| * 8 - threshold (can combine with 1-4) | * 8 - threshold (can combine with 1-4) | ||
| - | * | + | |
| NAME - save stats in file NAME, if specified | 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& | ||
| + | OFFROI: if FLAG& | ||
| + | IGNOREROI: if FLAG& | ||
| + | ONROI: if FLAG& | ||
| + | NLVLS: Number threshold levels to calculate separately (default=1, or 10 if FLAG& | ||
| - | NLVLS: Number threshold levels to calculate separately | + | Note: If you want a PREFIX without specifying output file NAME you must include a MASKVAL |
| If input is a Surface:\\ | If input is a Surface:\\ | ||
jvs/fscan/manual/chapter2/roistats.txt · Last modified: 2023/10/18 18:11 by voyvodic
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