Hello,
I'm preparing to do resting state analyses and I'd like to use the Yeo 2011 network atlas for the cortical parcellations. Looking through the archive, I know that mri_surf2surf with the -sval-annot flag can be used to convert the fsaverage from the Yeo et al 2011 study to an individual subject space, but I noticed a caveat to this when I called mri_surf2surf -help. The caveat is on example 5: "this is not a substitute for running the cortical parcellation! The parcellations that it maps to the new subject may not be appropriate for that subject."
Given this information, I've got a few questions:
1) How accurate is the mapping using mri_surf2surf? That is, is it good for preliminary data, but not for the final analysis?
2) How do you run the cortical parcellation using the Yeo 2011 atlas? [I know that mris_ca_train and mris_ca_label exist, but I'm unsure if they are the right commands to run when I'm not building my own atlas]
3) If I do the cortical parcellations using the Yeo 2011 atlas, will the edits/labels I've done using the Desikan atlas remain accurate? This goes back to the second question, as I'm not sure where in the general processing stage I need to go.
Thank you!
Sincerely,
Emma Bailin
Emma Bailin Research Coordinator Laboratory for Visual Neuroplasticity Schepens Eye Research Institute Mass. Eye and Ear Infirmary Harvard Medical School
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Hi Emma,
I recommend that you follow the mri_surf2surf and mri_label2vol route. As recommended in the other emails, you should probably load the resulting parcellations and make sure they look ok.
As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so applicable here because they require multiple subjects with resting-state parcellations in order to train the classifier. We are working on an individual subject 7-network and 17-network parcellation algorithm, but it's not ready yet.
What kind of edits have you already done? If your edits involve correcting the gray/white matter segmentation and the cortical surfaces, then your edits should be reflected (since mri_surf2surf and mri_label2vol should utilized the updated cortical surfaces). However, if your edits involving editing the Desikan's parcellation itself, then probably not.
Regards, Thomas
On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma Emma_Bailin@meei.harvard.edu wrote:
Hello,
I’m preparing to do resting state analyses and I’d like to use the Yeo 2011 network atlas for the cortical parcellations. Looking through the archive, I know that mri_surf2surf with the –sval-annot flag can be used to convert the fsaverage from the Yeo et al 2011 study to an individual subject space, but I noticed a caveat to this when I called mri_surf2surf –help. The caveat is on example 5: “this is not a substitute for running the cortical parcellation! The parcellations that it maps to the new subject may not be appropriate for that subject.”
Given this information, I’ve got a few questions:
How accurate is the mapping using mri_surf2surf? That is, is it goodfor preliminary data, but not for the final analysis?
How do you run the cortical parcellation using the Yeo 2011 atlas?[I know that mris_ca_train and mris_ca_label exist, but I’m unsure if they are the right commands to run when I’m not building my own atlas]
If I do the cortical parcellations using the Yeo 2011 atlas, willthe edits/labels I’ve done using the Desikan atlas remain accurate? This goes back to the second question, as I’m not sure where in the general processing stage I need to go.
Thank you!
Sincerely,
Emma Bailin
Emma Bailin
Research Coordinator
Laboratory for Visual Neuroplasticity
Schepens Eye Research Institute
Mass. Eye and Ear Infirmary
Harvard Medical School
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 844-815-4401. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
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Hi Emma,
I know it's been a long time, but my RA recently explored this and we think that mri_aparc2aseg might be a better option that mri_label2vol. Anyway, here's the updated process for mapping the Yeo2011 networks from fsaverage5 to individual volumetric space:
1) Transform from fsaverage to subject's surface mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh --sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval $SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot (repeat for rh)
2) Transform from subject's surface into your subject's volume Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg". This will give you ROIs that fully cover subject's grey matter.
mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o $SUBJECTS_DIR/yoursubject/mri/outputfile.mgz
One thing to note: "mri_aparc2aseg" will automatically add 1000 for left cerebral cortex voxels and add 2000 for right cerebral cortex voxels. Therefore, for example, a left hemisphere voxel in network 5 will have a value of 1005 in your outputfile.mgz. Here is our suggestion: a) Find the indices of left/right cerebral cortex by extracting the voxels with a value of 3 or 42 in the subject's aseg. b) Use those indices to mask out the voxels that are not cerebral cortex in your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0). c) For the cortical voxels, you may subtract 1000 for those between 1000 and 2000; and subtract 2000 for those greater than 2000.
Thanks, Thomas
On Wed, Feb 15, 2017 at 11:52 AM Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Emma,
I recommend that you follow the mri_surf2surf and mri_label2vol route. As recommended in the other emails, you should probably load the resulting parcellations and make sure they look ok.
As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so applicable here because they require multiple subjects with resting-state parcellations in order to train the classifier. We are working on an individual subject 7-network and 17-network parcellation algorithm, but it's not ready yet.
What kind of edits have you already done? If your edits involve correcting the gray/white matter segmentation and the cortical surfaces, then your edits should be reflected (since mri_surf2surf and mri_label2vol should utilized the updated cortical surfaces). However, if your edits involving editing the Desikan's parcellation itself, then probably not.
Regards, Thomas
On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma Emma_Bailin@meei.harvard.edu wrote:
Hello,
I’m preparing to do resting state analyses and I’d like to use the Yeo
2011
network atlas for the cortical parcellations. Looking through the
archive, I
know that mri_surf2surf with the –sval-annot flag can be used to convert
the
fsaverage from the Yeo et al 2011 study to an individual subject space,
but
I noticed a caveat to this when I called mri_surf2surf –help. The caveat
is
on example 5: “this is not a substitute for running the cortical parcellation! The parcellations that it maps to the new subject may not
be
appropriate for that subject.”
Given this information, I’ve got a few questions:
How accurate is the mapping using mri_surf2surf? That is, is itgood
for preliminary data, but not for the final analysis?
How do you run the cortical parcellation using the Yeo 2011atlas?
[I know that mris_ca_train and mris_ca_label exist, but I’m unsure if
they
are the right commands to run when I’m not building my own atlas]
If I do the cortical parcellations using the Yeo 2011 atlas, willthe edits/labels I’ve done using the Desikan atlas remain accurate? This goes back to the second question, as I’m not sure where in the general processing stage I need to go.
Thank you!
Sincerely,
Emma Bailin
Emma Bailin
Research Coordinator
Laboratory for Visual Neuroplasticity
Schepens Eye Research Institute
Mass. Eye and Ear Infirmary
Harvard Medical School
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use
of
the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this
e-mail is
strictly prohibited. If you believe you have received this e-mail in
error
and the email contains patient information, please contact the Mass. Eye
and
Ear Compliance Line at 844-815-4401. If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and delete the e-mail.
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@nmr.mgh.harvard.edu
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Bailin, Emma -
Thomas Yeo