Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks, Andrea B.
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Hi,
Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall be a different color or just not there/hole in the brain.
Best, Stephanie
Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078
Hi Stephanie
in tksurfer I think you can type:
mask_label lh.cortex
(or rh.cortex)
at the tcl (%) command line
cheers Bruce
On Thu, 7 Jan 2016, DeCross, Stephanie N. wrote:
Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall be a different color or just not there/hole in the brain.
Best, Stephanie
Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078
freeview partial solution
If this is important to you, you could write a quick script to do this for you:
1. mri_annotation2label to output all labels
2. write a script to launch freeview and load all of the labels (reading the color and applying it from the FS ctab file)
e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
3 you could then scroll through and click all of them off, and then click to load each one individually.
or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option).
hth d
On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce
On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thank you. This is helpful.
As to the broader question: is there truly no interactive, online atlas that uses either the Destrieux or Duvernoy parcellation scheme to examine the landmark boundaries with respect to, say, MNI space?
Thanks, Andrea
On 1/7/16, 4:26 PM, "dgw" dgwakeman@gmail.com wrote:
freeview partial solution
If this is important to you, you could write a quick script to do this for you:
mri_annotation2label to output all labels
write a script to launch freeview and load all of the labels
(reading the color and applying it from the FS ctab file)
e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
3 you could then scroll through and click all of them off, and then click to load each one individually.
or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option).
hth d
On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce
On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Andrea,
As far as I know no.
Additionally, i don't think it makes a lot of sense to do, because the two parcellations are created in fsaverage space, and while there are morphings etc. that are possible these tricks will always introduce errors etc. Additionally MNI space is defined in a completely different way to Freesurfer space, and so translating the one two the other is strange, because in FS you have locations on a surface while in MNI they are 3d coordinates. Occasionally frustrating reviewers demand MNI coordinates, likely not realizing that in that translation they are being provided with strange data, and we have to send them something, but overall, I find that picking the atlas/space which makes sense for that question is the best place to start.
hth d
On 1/9/16 12:40 PM, Andrea Bozoki wrote:
Thank you. This is helpful.
As to the broader question: is there truly no interactive, online atlas that uses either the Destrieux or Duvernoy parcellation scheme to examine the landmark boundaries with respect to, say, MNI space?
Thanks, Andrea
On 1/7/16, 4:26 PM, "dgw" dgwakeman@gmail.com wrote:
freeview partial solution
If this is important to you, you could write a quick script to do this for you:
mri_annotation2label to output all labels
write a script to launch freeview and load all of the labels
(reading the color and applying it from the FS ctab file)
e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
3 you could then scroll through and click all of them off, and then click to load each one individually.
or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option).
hth d
On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce
On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, but at the end of the day, we are talking about function of the same brain regions regardless of how they are created/defined. Can¹t do a meta-analysis, or a validation of reported locations from one method to the other without knowing whether one author's ³R anterior insula² encompasses another¹s ctx_rh_S_circular_insula_ant. Plus, the minute you take an ROI created by Freesurfer to analyze a PET image (which cannot be surface-rendered accurately due to its inherent low resolution), you are forced to ³translate² the borders of ROIs from FS to a coordinate-based scheme anyway. BTW- it is that latter problem I am trying to troubleshoot in my data.
I will try implementing your Freeview solution; thanks again.
Andrea B.
On 1/9/16, 5:42 PM, "dgw" dgwakeman@gmail.com wrote:
Hi Andrea,
As far as I know no.
Additionally, i don't think it makes a lot of sense to do, because the two parcellations are created in fsaverage space, and while there are morphings etc. that are possible these tricks will always introduce errors etc. Additionally MNI space is defined in a completely different way to Freesurfer space, and so translating the one two the other is strange, because in FS you have locations on a surface while in MNI they are 3d coordinates. Occasionally frustrating reviewers demand MNI coordinates, likely not realizing that in that translation they are being provided with strange data, and we have to send them something, but overall, I find that picking the atlas/space which makes sense for that question is the best place to start.
hth d
On 1/9/16 12:40 PM, Andrea Bozoki wrote:
Thank you. This is helpful.
As to the broader question: is there truly no interactive, online atlas that uses either the Destrieux or Duvernoy parcellation scheme to examine the landmark boundaries with respect to, say, MNI space?
Thanks, Andrea
On 1/7/16, 4:26 PM, "dgw" dgwakeman@gmail.com wrote:
freeview partial solution
If this is important to you, you could write a quick script to do this for you:
mri_annotation2label to output all labels
write a script to launch freeview and load all of the labels
(reading the color and applying it from the FS ctab file)
e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
3 you could then scroll through and click all of them off, and then click to load each one individually.
or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option).
hth d
On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce
On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 01/10/2016 12:20 PM, Andrea Bozoki wrote:
Plus, the minute you take an ROI created by Freesurfer to analyze a PET image (which cannot be surface-rendered accurately due to its inherent low resolution), you are forced to ³translate² the borders of ROIs from FS to a coordinate-based scheme anyway.
Not so fast. See for example Greve, et al, 2014. Cortical surface-based analysis reduces bias and variance in kinetic modeling of brain PET data
I will try implementing your Freeview solution; thanks again.
Andrea B.
On 1/9/16, 5:42 PM, "dgw" dgwakeman@gmail.com wrote:
Hi Andrea,
As far as I know no.
Additionally, i don't think it makes a lot of sense to do, because the two parcellations are created in fsaverage space, and while there are morphings etc. that are possible these tricks will always introduce errors etc. Additionally MNI space is defined in a completely different way to Freesurfer space, and so translating the one two the other is strange, because in FS you have locations on a surface while in MNI they are 3d coordinates. Occasionally frustrating reviewers demand MNI coordinates, likely not realizing that in that translation they are being provided with strange data, and we have to send them something, but overall, I find that picking the atlas/space which makes sense for that question is the best place to start.
hth d
On 1/9/16 12:40 PM, Andrea Bozoki wrote:
Thank you. This is helpful.
As to the broader question: is there truly no interactive, online atlas that uses either the Destrieux or Duvernoy parcellation scheme to examine the landmark boundaries with respect to, say, MNI space?
Thanks, Andrea
On 1/7/16, 4:26 PM, "dgw" dgwakeman@gmail.com wrote:
freeview partial solution
If this is important to you, you could write a quick script to do this for you:
mri_annotation2label to output all labels
write a script to launch freeview and load all of the labels
(reading the color and applying it from the FS ctab file)
e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
3 you could then scroll through and click all of them off, and then click to load each one individually.
or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option).
hth d
On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andrea
I'm not sure what you mean but I'm pretty certain the answer is "no".
sorry Bruce
On Thu, 7 Jan 2016, Andrea Bozoki wrote:
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)?
It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual).
Thanks,
Andrea B.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Andrea Bozoki -
Bruce Fischl -
DeCross, Stephanie N. -
dgw -
Douglas N Greve