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'''(formerly called mri_cor2label)'''

'''Index'''
<<TableOfContents>>


= Name =
mri_vol2label - converts values in a COR volume to a label. (formerly called mri_cor2label)

= Synopsis =
mri_vol2label --c <cordir> --id <labelid> --l <labelfile>

= Arguments =
== 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||

== Optional Flagged Arguments ==
|| --v  <volfile> || write label volume in file||
|| --help || print out help information||
|| --synth || synthesizes a label (ignores values in COR volume)||
|| --surf subject hemi <surf> || interpret input as a surface overlay ||
|| --sd subjectsdir || override $SUBJECTS_DIR ||

= Description =
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.

== Note ==
The name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).

= Examples =
== Example 1 ==
{{{
mri_vol2label --c /space/final/frontier/myparcellation --id 57 --l /home/brainmapper/spattemp/57.label
}}}
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 ==
Create a label of the left hemi surface vertices whose thickness is greater than 2mm.

First, create a binarized map of the thickness: 
{{{
mri_binarize --i $SUBJECTS_DIR/subject/surf/lh.thickness --min 2 --o lh.thickness.thresh.mgh

mri_cor2label --i lh.thickness.thresh.mgh --surf subject lh  --id 1 --l ./lh.thickness.thresh.label
}}}

= Bugs =
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.

= See Also =
[[tkmedit]], [[mri_label2label]]

= Links =
FreeSurfer, FsFast

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

= Author/s =
DougGreve