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| '''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 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''' - 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. |
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| || [options] || -u, -t, -w, -a, -f, -v, -ct, -file, -projfrac, -projmm, -proj, -trans, -replace, -fix, -surf, -sdir, -?, --version, --help || | || [options] || -u, -t, -w, -a, -f, -v, -ct, -file, -projfrac, -projmm, -proj, -trans, -replace, -fix, -surf, -sdir, --version, --help || |
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| || -? || print usage info || | |
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| mris_sample_parc | mris_sample_parc -ct FooColorLUT.txt subject01 lh subj01_parc_masks.mgz lh.parcmask.annot |
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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 [[LabelsClutsAnnotationFiles#head-e5ec66fee7ea903e9c03faa12cd076c541ad0a62|color table]] information in `FooColorLUT.txt` file, and is usually saved in `$SUBJECTS_DIR/$SUBJECT/label/` directory. |
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| ["mris_ca_train"] ["mris_ca_label"] |
[[mris_ca_train]] [[mris_ca_label]] |
Index
Contents
Name
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.
Synopsis
mris_sample_parc [options] <subject name> <hemi> <parc name> <output annot>
Arguments
Positional Arguments
[options] |
-u, -t, -w, -a, -f, -v, -ct, -file, -projfrac, -projmm, -proj, -trans, -replace, -fix, -surf, -sdir, --version, --help |
<subject name> |
the subject id |
<hemi> |
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) |
--help |
print help info |
--version |
print version info |
Outputs
<output annot> |
parcellation annotation output file |
Example
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.
Bugs
None
See Also
Links
CorticalParcellation, FreeSurfer, FsFast
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>