mris_sample_parc - Samples a volumetric parcellation onto a surface. Manual labeling can be carried out directly on surface models using drawing tools in tksurfer, or volumetrically in tkmedit, then sampled onto the surfaces using mris_sample_parc. mris_ca_train is used to create an atlas from a set of annotated subjects. The information output by mris_ca_train is then used by mris_ca_label to automatically assign a neuroanatomical label to each location on a cortical surface model. Note that an "annotation" is synonymous with a "parcellation", and is used for backwards compatibility.


mris_sample_parc [options] <subject name> <hemi> <parc name> <output annot>


Positional Arguments


-u, -t, -w, -a, -f, -v, -ct, -file, -projfrac, -projmm, -proj, -trans, -replace, -fix, -surf, -sdir, --version, --help

<subject name>

the subject id


hemisphere: rh or lh

<parc name>

parcellation filename

<output annot>

annotation filename

Required Flagged Arguments

<subject name> <hemi> <parc name> <output annot>

Optional Flagged Arguments

-sdir <directory>

use <directory> as subjects directory (default: $SUBJECTS_DIR)

-surf <filename>

use <filename> as surface (default: 'white')

-fix <number>

fix topology of all labels smaller than <number> vertices (default=-1, do all)

-replace <number>

replace label <number> with deeper ones

-trans <number_in> <number_out>

translate <number_in> to <number_out>

-projmm <number>

project <number> millimeters along surface normal (default=0.0)

-proj <number>

same as -projmm

-projfrac <number>

project <number> percent along surface normal (default=0.5)

-file <filename>

use <filename> as translation (default: 'cma_parcellation_colors.txt')

-ct <filename>

embed color table <filename> into output annotation file

-v <number>

diagnostic level (default=0)

-f <number>

apply mode filter <number> times to parcellation (default=0)

-a <number>

smooth surface <number> times (default=0)

-w <number>

use window size <number> for sampling (default=7)

-t <filename>

use thickness file <filename> (default: 'thickness')

-u <number>

change largest connected unknown region to label <number> (default: don't change)


print help info


print version info


<output annot>

parcellation annotation output file


mris_sample_parc -ct FooColorLUT.txt subject01 lh subj01_parc_masks.mgz lh.parcmask.annot

This samples the volumetric parcellation subj01_parc_masks.mgz as an annotation lh.parcmask.annot for the subject subject01's left hemisphere. The output annotation is embedded with the color table information in FooColorLUT.txt file, and is usually saved in $SUBJECTS_DIR/$SUBJECT/label/ directory.



See Also

mris_ca_train mris_ca_label


CorticalParcellation, FreeSurfer, FsFast


Reporting Bugs

Report bugs to <>



mris_sample_parc (last edited 2008-11-17 15:18:17 by KrishSubramaniam)