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--- jvs:fscan:manual:chapter2:roi [2015/06/06 19:33]
voyvodic
+++ jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current)
@@ Line 2: / Line 2: @@
 ===== ROI -- Define and manipulate Regions of Interest =====
 ====usage:====
+[[jvs:fscan:manual:chapter2:addroi|Adding new ROIs]]\\
   * -roi POINT [NAME] x y z\\
   * -roi BLOCK [NAME] x0 y0 z0 nx ny nz\\
@@ Line 15: / Line 16: @@
   * -roi TEXT [NAME] textstring x0 y0 x1 y1
   * -roi MASK datasetname
+  *
   * -roi FILE roifile
   * -roi RX refimage  (not yet implemented)
-  * -roi MEAN flag
+  * -roi AVERAGE flag radiusMM thresh
+  * -roi HEAD [NAME] flag
+     Create BLOCK roi by auto-detection of top, sides, & front/back of head.
+     Arbitrarily set bottom by making I-S distance same as R-L.
+      FLAG: 0 - default (bottom boundary set at top - (L/R distance)
+-
+- set intensity threshold at 10% of maxval (default is 15%)
+- set     "         "     "  20%
+             ...
+- set     "         "     "  70%
+  * -roi ALIGN [refimage flag refroi thisroi]
+     Generate affine matrix (align or wsalaign) to align current images
+     to REFIMAGE dataset by scaling and translating THISROI to match REFROI.
+       REFIMAGE - data set to align to (prevwin by default)
+       FLAG - option flag (default = 0)
+       REFROI - name or ROINUM for REFIMAGE roi to use
+                (default is active or first ROI)
+       THISROI - name or ROINUM for current image roi
+                (default is active or first).
+     Example usage is to align head rois (see: -roi HEAD)
+[[jvs:fscan:manual:chapter2:roicorrel|Generate ROI correlations]]\\
   * -roi CORREL flag refROI binsize corrROI name thresh
+[[jvs:fscan:manual:chapter2:clusters|Cluster ROIs]]\\
   * -roi CLUSTER refimage flag name
   * -roi MERGE refimage flag name minvalley minsize mindist
+[[jvs:fscan:manual:chapter2:roistats|Generate ROI statistics]]\\
   * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel
+  * -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh
-[[jvs:fscan:manual:chapter2:addroi|Adding new ROIs]]
 [[jvs:fscan:manual:chapter2:editroi|Modifying ROIs]]
-[[jvs:fscan:manual:chapter2:clusters|Cluster ROIs]]
-[[jvs:fscan:manual:chapter2:roistats|Generate ROI statistics]]
-ROI's can be added to the current data set by explicitly specifying the ROI type, location, and size. The list above shows the various ROI types and how they are specified. The meaning of he arguments is:
-  * NAME - specify a name for this ROI (no spaces or punctuation)
-  * X0,Y0,Z0 - specify the starting location of the ROI as upper left corner of the first slice. The default origin is 0,0,0.
-  * NX,NY,NZ - specify the size of the ROI. The default size is 1x1x1 (i.e. a point) if X0,Y0,Z0 are specified, otherwise it is the entire volume.
-  * RAD,RADX,RADY,RADZ - specify radii for circular ROIs
-  * COLOR - specify color for ROI (24-bit RGB value)
 The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE.
@@ Line 59: / Line 80: @@
 	NAME: name of ROI list. If omitted, list is linked to
           input mask images.
--roi MERGE refimage flag name minvalley minsize mindist
+-roi MERGE refimage flag name minval minsize mindist
-The MERGE command assumes that the current image is an ROI mask.
+Assumes input data set is roi mask image with an ROI cluster list
+(usually made with ROI CLUSTER command). The ROI MERGE command
+allows you to modify the input data set and/or its Cluster list.
-MERGE edits the ROI list. Merge adjacent clusters if:
+Merge can be used in different ways (controlled by FLAG):
-) distance bet peaks < MINDIST
-) stat value in valley between peaks is within MINVALLEY percent of lower peak
+  FLAG 1 - Merge adjacent clusters if:
-) smaller cluster contains fewer than MINSIZE voxels
+) distance bet peaks < MINDIST
+) stat value in valley between peaks is within MINVAL percent of lower peak
+) smaller cluster contains fewer than MINSIZE voxels
+  FLAG 2 - Compare input cluster list to REFIMAGE cluster list.
-  FLAG: 2 - do not modify input mask image values when editting ROI list
+  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.
-   (i.e. if merging ROI clusters, change merged mask values)
-  NAME: name of ROI list. If omitted, list is linked to input mask images.
+  REFIMAGE is the reference data set; the type of data depends on FLAG:
-  MINVALLEY: (default= 60% of lower peak maximum)
+    FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
-  MINSIZE: (default= 5 voxels)
+    FLAG 2 - REFIMAGE is another mask image with attached cluster list.
-  MINDIST: (default= 40 mm)
+    FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
+    FLAG 4 - Remove clusters containing less than MINVAL voxels
+    FLAG 5 - Use REFIMAGE to adjust cluster index values. For each cluster, find
+             REFIMAGE mask value (REFVALUE) at cluster center. New cluster index is:
+                     REFVALUE * MINVAL + I
+             where I starts at 1 and increments to ensure each cluster has unique index.
--roi STATS refimage flag showflag mode name value nlevels level0 dlevel
+  Other FLAG values:
+- do not modify input mask image values when editting ROI list; by default
+        when ROI clusters are merged or cluster VALUEs are changed, the corresponding
+        image voxel values are also changed to match the new cluster VALUEs.
+- sort cluster list values by peak location (LPI -> RAS)
+- sort cluster list by cluster size (largest to smallest)
+  NAME: name of ROI list. If omitted, list is linked to input mask images.
+-roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\
+-roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh  (if flag TIMESERIES)
-Calulate stats in input data by ROI
+Calculate stats in input data by ROI
   REFIMAGE - dataset to use as ROI mask(s)
   FLAG - stats options (select one value 0-7; add other values)
@@ Line 91: / Line 131: @@
 - include peak val&loc, and above
 - include intensity weighted ctr loc, and above
-- mean time course
+- TIMESERIES; calculate mean time course
 - calculate laterality index if available
 - calculate stats omitting zero values
 - report ROI volumes in mm3 (voxel count X voxel volume)
 - include ROI's with only zero values (usually ignored)
+- WEIGHTED; weight stats by mask value
+- no threshold
+- CYCLES; calculate time-series stats by task cycle
+- BINARYMASK; consider all non-zero voxels in mask as single ROI
   SHOWFLAG - Report generation flags
 - tab-separated columns in text output
@@ Line 118: / Line 163: @@
   NAME - save stats in file NAME, if specified
   VAL: if > 0, only calculate for this mask value
-  NLVLS: # threshold levels to calc separately (def=1)
+  If FLAG & 02010, time-series by CYCLE,
-If input is a Surface:
+    CYCLELENG: task cycle length in secs
+    CYCLEOFF: first cycle offset in secs (ignore images before this)
+    THRESH: mask threshold (assumes WEIGHTED and BINARYMASK)
+  otherwise,
+    NLVLS: # threshold levels to calc separately (def=1)
+    LEVEL0: first threshold level (def=0)
+    DLEVEL: increment between levels (def=1)
+  If input is a Surface:
   FLAG
 - surface area of AREA ROI or path length of contour ROI
--roi CORRELATE flag ref_roi binsize corr_roi name thresh
+**See Also:**\\
+[[jvs:fscan:manual:chapter2:addroi|Create ROIs]],
+[[jvs:fscan:manual:chapter2:editroi|Edit ROIs]],
+[[jvs:fscan:manual:chapter2:clusters|Clusters]],
+[[jvs:fscan:manual:chapter2:roistats|ROI Stats]]
-Generate new data set (named NAME) containing multiple
-correlation maps based on correlating the time course for
-each voxel within the REFROI in the current data set
-with each voxel in the CORR_ROI. The 2 ROI's can be the same;
-by default they are the entire data set volume.
-FLAG can be used for specifying options:
-- generate neighbor correlation map. Correlates each voxel time course with
-      its 26 neighbors and saves the mean correlation coefficient.
-- do not mask out low intensity values (by default CORRELATE assumes the -m command)
-- use REFROI as CORR_ROI as well
-REFROI can be the name of an ROI, or it can be:
-- use the default: 5 if FLAG&
-- use the time course at the current voxel as reference
-- use the current point ROI time course as reference
-- use every voxel within the current box roi as a separate reference (this generates
-map per ref voxel; the ref voxel in each  map will have correl value of 1.0)
-- use every voxel in all active ROI's in this data set
-- use every voxel in the volume
-  <0 - Negative ROINUM - specify any active ROI by the negative of its ROINUM\\
-  Default is 3 if there is a box ROI, otherwise it is 1
-BINSIZE is how many voxels in each dimension to bin together
-for reference (default=1).
-CORR_ROI is the ROI to use as a mask for which voxels to test.
-By default,CORR_ROI is the entire data set.  Like REFROI,
-CORR_ROI can be the name of an ROI, or it can be:
-- default. same as 5
-- use REFROI as CORR_ROI
-- use the current box roi as CORR_ROI
-- correlate with voxels in all active ROI's in this data set
-- correlate with every voxel in the data set volume (default)
-  <0 - Negative ROINUM - specify any active ROI by the negative of its ROINUM
-NAME is the name of the output data set; default adds suffix
-roicorrel to current data set name.
-THRESH is the auto-correlation threshold for counting neighboring
-voxels as positively correlated (default=0.3)
-**See Also:**\\
 [[jvs:fscan|fScan Home]],
 [[jvs:fscan:manual|fScan Manual]],
 [[jvs:fscan:manual:chapter2|CmdLineOptions]],
 [[jvs:fscan:manual:help|Manual Help]]

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