Hi experts,
I’m trying to create a pretty picture via Freesurfer / freeview. Specifically, I have 6 regions that I want to combine into 2 rois (1 color for each 3-region-roi ) that would display over a gray-background. So in Freeivew, my goal is to see a gray pial surface with roiA displayed in red and roiB displayed as blue with all other labels present, but gray.
I’ve already read through the FAQ and attempted what I’ve seen work for others, but I seem to be hitting some kind of trouble and I’m not sure which steps / flags to adjust…
Here is what I’ve tried so far:
1) mri_annotation2label –surf pial –hemi rh –outdir ./roi
a. This got me all my rh.label files …
2) Then I used: mri_mergelabels –i rh.insula.label –i rh.fusiform.label –i rh.isthmuscingulate.label –o rh.ins_fus_icing.label (and repeat this for the next roi, using different labels)
a. This got me a 2 new .label files that overlay great in Freeview if I load them individually on the rh.pial surface. The problem is that I can only seem to load ONE label at a time for the overlay, which does not meet my goal. So, to load multiple labels I tried combining them via…
3) mris_label2annot --s $code --hemi rh --ctab /home/vhasfcbuckls/Freesurfery/$code/label/roi/roi_added_bgGray.aparc.annot.ctab \
--a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/$code/label/roi/rh.ins_fus_icing.label \
--l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_tpole_parah.label
I’ve attached 2 screenshots: one where I’ve successfully loaded just ONE of the ROIs on the rh.pial (roiA_label_loaded.png); the other shows what I see after loading the product from step3 (annot_loaded_roiAB_graybg.png), which shows all 6 regions, but they aren’t grouped into 2 rois by color, and the background is black instead of gray. The annotation seems to think I only have the 2 regions indicated in the std out (below), which is unexpected. I feel like there is some flag I’m missing here…
I’ve attached the modified ctab file used as an input to mris_label2annot, wherein I’ve appended my custom labels to the standard aparc.annot.ctab and assigned new RGB colors. All other regions were changed to 127 127 127 0 to make them gray.
Question:
Can you please tell me which steps / flags/ inputs that need adjustments in order to reach my goal? Or is there a better tool / method that I should use for this visualization instead?
Please let me know if you need more information.
Thanks very much for your time,
~Shannon
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Here is the std out for step3:
mris_label2annot --s $code --h rh --ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_added_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_fus_icing.label --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_tpole_parah.label
Using Freesurfer version 5.1.
Subjects Directory is /home/vhasfcbuckls/Freesurfery
Sessions Directory is /home/vhasfcbuckls/sessions
Reading ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_added_GrayBG.aparc.annot.ctab
Number of ctab entries 38
$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi
cmdline /opt/freesurfer5.1/bin/mris_label2annot --s PPMI_012_S_3181m00_i357579 --h rh --ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_added_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_fus_icing.label --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_tpole_parah.label
sysname Linux
hostname london.v21.med.va.gov
machine x86_64
user vhasfcbuckls
subject PPMI_012_S_3181m00_i357579
hemi rh
SUBJECTS_DIR /home/vhasfcbuckls/Freesurfery
ColorTable /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_added_GrayBG.aparc.annot.ctab
AnnotName newrois.graybg.aparc
nlables 2
LabelThresh 0 0.000000
Loading /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/surf/rh.orig
1 8355711 bankssts
2 8355711 caudalanteriorcingulate
Mapping unhit to unknown
Found 114343 unhit vertices
Writing annot to /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/rh.newrois.graybg.aparc.annot
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