Name
mri_vol2roi - extracts ["ROI"] from volume
Synopsis
mri_vol2roi
Default Flagged Arguments
--srcvol |
input volume path |
--srcreg |
source registration (SrcXYZ = R*AnatXYZ) |
--label |
path to label file |
--labelreg |
label registration (LabelXYZ = L*AnatXYZ) |
- See warning before using this option.
--labeltal |
use tal xfm for labelreg |
--talxfm |
use talxfm intead of talairach.xfm |
--labelfillthresh thresh |
fraction of voxel |
--mskvol |
mask volume path |
--mskthresh |
threshold (0.5) mask threshold |
--msktail |
'<abs>', pos, or neg (mask tail) |
--mskframe |
0-based mask frame <0> |
--mskinvert |
invert the mask |
--roiavgtxt |
fname :output text file for ROI average |
--roiavg |
stem : output bfloat stem for ROI average |
--finalmskvol |
path in which to save final mask |
--finalmskcrs |
fname save col,row,slice in text fname |
Positional Arguments
[argA] |
description |
Required Flagged Arguments
-flag1 [arg1] |
description |
-flag2 [arg2] |
description |
Optional Flagged Arguments
-flag3 [arg3] |
description |
-flag4 [arg4] |
description |
Outputs
volume1 |
description |
volume2 |
description |
Description
["mri_vol2roi"] extracts a region-of-interest (["ROI"]) from a volume. The ROI can be defined in one of three ways: (1) as set of voxels in a mask volume the same size as the source volume, (2) as a set of label points (defined in a label file), or (3) the intersection of (1) and (2). mri_vol2roi can also be used to create a binary mask volume from a label; see CREATING A BINARY MASK VOLUME FROM A LABEL below.
The result is a text file (argument of --roiavgtxt) with the following rows of information. (1) The number of source voxels in the label (0 if no label is used). (2) The number of voxels in the final ROI. (3) the average of the ROI voxels in the source volume. If the source volume has multiple frames, then there will be a row for each frame.
In addition, a final ROI mask volume can be saved. This volume is the same size as the source volume (one frame only). The value of a voxel is 1 if it was in the final ROI or 0 if it was out.description
Detailed Flag Description
-flagAlpha [a]
-flagBravo [b]
Examples
Example 1
mri_vol2roi foo -i f -o out
description
Example 2
mri_vol2roi foo -i f -o out -f fvalue
description
See Also
["othercommand1"], ["othercommand2"]
Links
FreeSurfer, FsFast, ["ROI"]
Methods Description
None
References
None
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>