Hi,
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 .
I have 2 questions:
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?
Thanks, Andrea
[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.govapplewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov
