I am trying to show 3 aparc labels on the inflated surface, each in a different color, let’s say lh.inferiortemporal, lh.middletemporal and lh.superiortemporal .

First I ran mris_annotation2label to extract the individual region aparc labels.

I can merge them into a single label with mri_mergelabels, but when I do this both regions are in the same color.

I alternatively tried mris_label2annot, as follows:

mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label

Question 1) Should I be concerned that it says “bankssts, caudalanteriorcingulate, and caudalmiddlefrontla” in the output (copied below) and the freeview windw (see attached) even though I see ITG/MTG/STG on the brain in free view?

Question 2) But, when I show the annotation file on the inflated brain in freeview, I can see the three region in 3 different colors, but the rest of the brain is a dark purple and hard to see. See attached image. Is there a way to change this so it looks like the inflated brain typically does?

Or, is it possible to view more than one individual label at once?

[goldal2@biowulf label]$ mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label

Reading ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab

Number of ctab entries 36

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $

cwd /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label

cmdline mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label

sysname Linux

hostname biowulf.nih.gov

machine x86_64

user goldal2

subject fsaverage

hemi lh

SUBJECTS_DIR /data/EDAN/freesurfer/buckner_data/tutorial_subjs

ColorTable /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab

AnnotName LeftTemporal_test

nlables 3

LabelThresh 0 0.000000

Loading /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/surf/lh.orig

1 2647065 bankssts

2 10511485 caudalanteriorcingulate

3 6500 caudalmiddlefrontal

Mapping unhit to unknown

Found 147704 unhit vertices

Writing annot to /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/lh.LeftTemporal_test.annot

Andrea Gold, Ph.D.

Section on Development and Affective Neuroscience

National Institute of Mental Health
Room 201, Bldg. 15K, MSC 2670
Bethesda, MD 20892-2670
Phone: 301-827-9804
Fax: 301-402-2010

Email: andrea.gold@nih.gov