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_adde d_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_f us_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_adde d_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_adde d_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_f us_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_adde d_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.g raybg.aparc.annot
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Hi Shannon
not sure about freeview, Ruopeng should be able to answer that part, but it should be easy enough in tksurfer. Just load the labels separately and give them whatever color you want.
cheers Bruce
On Mon, 21 Jul 2014, Shannon Buckley 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_add ed_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_add ed_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_add ed_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_add ed_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
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Aha Tksurfer, of course!
Will follow up with Ruopeng about freeview, but tksurfer satisfies the goal nicely...
Thank you!
On Jul 22, 2014, at 7:53 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shannon
not sure about freeview, Ruopeng should be able to answer that part, but it should be easy enough in tksurfer. Just load the labels separately and give them whatever color you want.
cheers Bruce
On Mon, 21 Jul 2014, Shannon Buckley 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:
mri_annotation2label –surf pial –hemi rh –outdir ./roia. 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_add ed_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_add ed_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_add ed_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_add ed_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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Hi all,
I was wondering how you go about looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines in freeview?
Emily
Hi Emily - Actually, there is a bug in the 5.3 version of freeview in that specific feature. But you can use fslview - you select the V1 file, click on the (i) button and choose Display as: Lines.
a.y
On Tue, 22 Jul 2014, ebelleau@uwm.edu wrote:
Hi all,
I was wondering how you go about looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines in freeview?
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.buckley@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:
mri_annotation2label –surf pial –hemi rh –outdir ./roia. 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
Hi Ruopeng,
I just used the GUI while trying to figure this out... Was going to circle back to build a proper cmd line once I have the pieces I need. I was wondering if maybe my commands to build the annotation were faulty, but if it's just the version at issue then that's not so bad...
In any case, I loaded the rh.pial, then used the drop downs to load a label. I did the same with the annotation once I realized I could only load one label at a time. The annotation seemed "wrong" but perhaps it's just the display issue.
I'll see whether we can install the dev-build here since I usually use the official releases...
Thanks Ruopeng!
-Shannon
On Jul 22, 2014, at 8:00 AM, "Ruopeng Wang" <rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu> wrote:
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.buckley@ucsf.edumailto:shannon.buckley@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
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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.govhttp://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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<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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Anastasia Yendiki -
Bruce Fischl -
Buckley, Shannon -
ebelleau＠uwm.edu -
Ruopeng Wang -
Shannon Buckley