Name

mri_extract_label - extracts a set of labeled voxels from an image.

Synopsis

mri_extract_label [options] <input volume> <label 1> <label 2> ... <output name>

Arguments

Optional Flagged Arguments

-s <sigma>	apply a Gaussian smoothing kernel
-t <xform file>	apply the transform in <xform file> to extracted volume
-exit_none_found	exit 1 if label(s) are not found
-dilate <n>	dilate output volume <n> times
-erode <n>	erode output volume <n> times

Outputs

Description

This program will extract a set of labeled voxels from an image.

Examples

Bugs

Links

FreeSurfer

Methods Description

References

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-## page was renamed from mri_cor2label
-Line 10:
+Line 9:
-'''(formerly called mri_cor2label)'''
-Line 17:
+Line 15:
-mri_vol2label - converts values in a COR volume to a label. (formerly called mri_cor2label)
+mri_extract_label - extracts a set of labeled voxels from an image.
-Line 20:
+Line 18:
-mri_vol2label --c <cordir> --id <labelid> --l <labelfile>
+mri_extract_label [options] <input volume> <label 1> <label 2> ... <output name>
-Line 23:
+Line 21:
-== Positional Arguments ==

none



== Required Flagged Arguments ==

|| --c <cordir> || directory to find COR volume||

|| --id <labelid> || 0-255 value in COR volume||

|| --l <labelfile> || name of output file||
-Line 32:
+Line 23:
-|| --v  <volfile> || write label volume in file||

|| --help || print out help information||

|| --synth || synthesizes a label (ignores values in COR volume)||
+|| -s  <sigma> || apply a Gaussian smoothing kernel ||

|| -t <xform file> || apply the transform in <xform file> to extracted volume ||

|| -exit_none_found || exit 1 if label(s) are not found ||

|| -dilate <n> || dilate output volume <n> times ||

|| -erode <n> || erode output volume <n> times ||
-Line 38:
+Line 31:
-[[mri_vol2label]] converts values in a COR volume to a label. The program searches the

COR volume in directory 'cordir' for values equal to 'labelid'. The

xyz values for each point are then computed assuming 1 mm^3 voxels and

that xyz=0 at the center of the volume. The xyz values are then stored

in 'labelfile' in the label file format; the vertex values are set to

zero as is the statistic value.  While this program can be used with

any COR volume, it was designed to convert parcellation volumes, which

happen to be stored in COR format.  See tkmedit for more information

on parcellations. The labelid must be within the range of 0 to 255.

The label volume in mm^3 can be written to the argument of --v.
+This program will extract a set of labeled voxels from an image.
-Line 50:
+Line 34:
-== Example 1 ==

mri_vol2label --c /space/final/frontier/myparcellation --id 57 --l /home/brainmapper/spattemp/57.label
-Line 53:
+Line 35:
-This will load the COR volume found in the directory /space/final/frontier/myparcellation and then search the volume for

values equaling 57.  The results are stored in 57.label in the directory /home/brainmapper/spattemp, which must exist prior to execution.



== Example 2 ==

??
-Line 60:
+Line 37:
-If the name of the label does not include a forward slash (ie, '/') then the program will attempt to put the label files in $SUBJECTS_DIR/subject/label.  So, if you want the labels to go into the current directory, make sure to put a './' in front of the label.
-Line 63:
+Line 40:
-[[tkmedit]], [[mri_label2label]]
-Line 66:
+Line 43:
-FreeSurfer, FsFast
+FreeSurfer
-Line 78:
+Line 55:
-DougGreve