Hi Shannon, If I understand correctly, you are trying to load 2 ROIs on top of a layer of annotations on surface? Can you show me the freeview command you run? Or did you do everything on the GUI? BTW, are you using the latest dev build of freeview or the released one in v5.3? If I remember correctly, the dev build fixed some annotation display bugs.
Best, Ruopeng On Jul 21, 2014, at 6:34 PM, Shannon Buckley <shannon.buck...@ucsf.edu> wrote: > 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 > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > 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 > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > <mris_label2annot_stdout.txt><annot_loaded_roiAB_graybg.png><roiA_label_loaded.png><roi_added_GrayBG.aparc.annot.ctab>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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