jvs:fscan:manual:chapter2:roistats
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jvs:fscan:manual:chapter2:roistats [2023/02/23 18:43] – external edit 127.0.0.1 | jvs:fscan:manual:chapter2:roistats [2023/10/18 18:09] – [-roi stats] voyvodic | ||
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* -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==== | ||
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* 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 | ||
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* 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: 2024/06/21 15:44 by 127.0.0.1