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jvs:fscan:manual:chapter2:editroi

fScan Reference Manual, Chapter 2 (CmdLineOptions): editroi

ROI -- Edit existing Regions of Interest

usage:

  • -roi TEXT [NAME] textstring x0 y0 z0 x1 y1 z1
  • -roi TEXT [NAME] textstring x0 y0 x1 y1
  • -roi MASK datasetname
  • -roi FILE roifile
  • -roi RX refimage (not yet implemented)
  • -roi MEAN flag
  • -roi CORREL flag refROI binsize corrROI name thresh
  • -roi CLUSTER refimage flag name
  • -roi MERGE refimage flag name minvalley minsize mindist
  • -roi STATS refimage flag showflag mode name value nlevels level0 dlevel

For manipulating existing ROIs:

The ROI command can also be used to manipulate existing ROI's.

-roi CLUSTER refimage flag name

	Assumes roi mask image as input. 
Create an ROI list (name=NAME) of clusters where each 
  cluster is defined by its mask value. For each cluster, 
  store center-of-mass and radius along principal axes. 
If REFIMAGE, find peak intensity value and voxel location. 
By default, ROI list is attached to input mask images.  
FLAG: (no values yet) 
 
NAME: name of ROI list. If omitted, list is linked to  
        input mask images. 

-roi MERGE refimage flag name minvalley minsize mindist

The MERGE command assumes that the current image is an ROI mask.

MERGE edits the ROI list. Merge adjacent clusters if:

1) distance bet peaks < MINDIST  
2) stat value in valley between peaks is within MINVALLEY percent of lower peak 
3) smaller cluster contains fewer than MINSIZE voxels 
 
FLAG: 2 - do not modify input mask image values when editting ROI list 
 (i.e. if merging ROI clusters, change merged mask values) 
 
NAME: name of ROI list. If omitted, list is linked to input mask images. 
MINVALLEY: (default= 60% of lower peak maximum) 
MINSIZE: (default= 5 voxels) 
MINDIST: (default= 40 mm) 
 

-roi STATS refimage flag showflag mode name value nlevels level0 dlevel

Calulate 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) 
     0 - default stats (3 = Mean,Count,StDev) 
     1 - include mean 
     2 - include counts, and mean 
     3 - include stdev, and above 
     4 - include range, and above 
     5 - include ctr loc, and above 
     6 - include peak val&loc, and above 
     7 - include intensity weighted ctr loc, and above 
   010 - mean time course 
   020 - calculate laterality index if available 
   040 - calculate stats omitting zero values 
  0100 - report ROI volumes in mm3 (voxel count X voxel volume) 
  0200 - include ROI's with only zero values (usually ignored) 
SHOWFLAG - Report generation flags 
     1 - tab-separated columns in text output 
         (default is space-separated) 
     2 - comma-separated columns in text output 
  0100 - save as XML text file 
  0200 - save as tab-delimited text file 
  0400 - plot ref time series 
 01000 - save as ref time series 
 02000 - generate AMPLE statistics 
 04000 - ignore thresholds (default: use threshold if active) 
010000 - Watch flag (?) 
 
MODE 
     0 - default: 1 if active ROI, 2 if this has glossary, 
         3 if prev has glossary, 4 if prev is atlas 
     1 - block ROI's (active or all) 
     2 - mask values in current data 
     3 - mask values in prev data set 
     4 - atlas areas 
     8 - threshold (can combine with 1-4) 
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 input is a Surface:

FLAG 
  1 - surface area of AREA ROI or path length of contour ROI 
   

-roi CORRELATE flag ref_roi binsize corr_roi name thresh

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:

1 - generate neighbor correlation map. Correlates each voxel time course with 
    its 26 neighbors and saves the mean correlation coefficient.  
2 - do not mask out low intensity values (by default CORRELATE assumes the -m command) 
4 - use REFROI as CORR_ROI as well 

REFROI can be the name of an ROI, or it can be:

0 - use the default: 5 if FLAG& 
1 - use the time course at the current voxel as reference 
2 - use the current point ROI time course as reference 
3 - use every voxel within the current box roi as a separate reference (this generates  
    1 map per ref voxel; the ref voxel in each  map will have correl value of 1.0) 
4 - use every voxel in all active ROI's in this data set 
5 - 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:

0 - default. same as 5 
1 - use REFROI as CORR_ROI 
3 - use the current box roi as CORR_ROI  
4 - correlate with voxels in all active ROI's in this data set 
5 - 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:
ROIs,
Edit ROIs,
Clusters,
ROI Stats

fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help

jvs/fscan/manual/chapter2/editroi.txt · Last modified: 2015/06/06 19:44 by voyvodic