Hi Josh,
Thanks for your interest. The networks are in MNI152 space. My understanding is that you want to map the networks onto the structural T1 data of your subjects. Here's my suggestion on how to do it:
1) Assuming you are quite happy with the freesurfer recon-all of your individual subjects, then this means that freesurfer nonlinear (volumetric) registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) First sample C1-C12 (Yeo_components2mm.nii.gz) to norm.mgz of MNI152_FS (because C1-C12 are 2mm, but norm.mgz is 1mm isotropic):
setenv SUBJECTS_DIR <something> mri_vol2vol --mov Yeo_components2mm.nii.gz --s MNI152_FS --targ <something>/MNI152_FS/mri/norm.mgz --regheader --o Yeo_components1mm.nii.gz
b) Warp the Yeo_components1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov Yeo_components1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo_components_internal_space.nii.gz
c) Warp Yeo_components_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS --targ Yeo_components_internal_space.nii.gz --m3z talairach.m3z --o Yeo_components_subject_space.nii.gz --interp nearest --inv-morph
This is not optimal because of the multiple interpolation, but the networks are quite smooth anyway, so it should be ok.
You might want to use the FSL MNI152 2mm template instead of Yeo_components2mm.nii.gz to test the steps above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use Yeo_components2mm.nii.gz. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Wed, May 18, 2016 at 3:53 AM, Josh Gray jgray7700@gmail.com wrote:
Hello,
I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this?
Thank you, Josh Gray
-- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia
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.