Hi Professor Yeo,
Thanks for providing a link to your split region MNI space files.
Could you please advise on how to get these labels into subject native space?
If using the standard version of the network labels that comes packaged with Freesurfer 5.3.0, I can get the annotation file into native space quite easily with the following command:
mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
However, in the dropbox link you posted, it doesn't seem that there is a .annot file compatible with fsaverage. The fsaverage5 version is present, but if I try slotting the fsaverage5 .annot file into the above call to mri_surf2surf, I get disastrous results.
Do you perhaps have a .annot file for the upsampled (and split) network labels? Or perhaps there's an easier way to achieve what I'm after. I notice that you have provided a .nii file for the network ROIs that is in the same space as fsaverage, perhaps this file can be warped to native space somehow?
Best wishes,
Richard Parker King's College London
Hi Erica,
You can try this link:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Spl...
Regards,
Thomas
On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung orange...@gmail.com wrote:
Dear Prof. Yeo,
I would like to extract the brain regions of the functional canonical
network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have
provided the split regions of 7&17 Network in previous discussion string.
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
)
However, the dropbox download link you offered has expired.
Would you mind uploading it again?
Thank you very much.
Erica
Hi Richard,
Sorry. My original reply was rejected by the list. Resending.
In the mri_surf2surf command, Instead of the srcsubject being fsaverage, can you try using the srcsubject as fsaverage5 instead?
Alternatively, you can try running mri_surf2surf twice. Once to upsample the fsaverage5 annot to fsaverage and then run the mri_surf2surf command from your email. (This might actually work better).
Thanks, Thomas
On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard richard.r.parker@kcl.ac.uk wrote:
Hi Professor Yeo,
Thanks for providing a link to your split region MNI space files.
Could you please advise on how to get these labels into subject native space?
If using the standard version of the network labels that comes packaged with Freesurfer 5.3.0, I can get the annotation file into native space quite easily with the following command:
mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
However, in the dropbox link you posted, it doesn’t seem that there is a .annot file compatible with fsaverage. The fsaverage5 version is present, but if I try slotting the fsaverage5 .annot file into the above call to mri_surf2surf, I get disastrous results.
Do you perhaps have a .annot file for the upsampled (and split) network labels? Or perhaps there’s an easier way to achieve what I’m after. I notice that you have provided a .nii file for the network ROIs that is in the same space as fsaverage, perhaps this file can be warped to native space somehow?
Best wishes,
Richard Parker
King’s College London
Hi Erica,
You can try this link:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Spl...
Regards,
Thomas
On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung orange...@gmail.com wrote:
Dear Prof. Yeo,
I would like to extract the brain regions of the functional canonical
network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have
provided the split regions of 7&17 Network in previous discussion string.
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
)
However, the dropbox download link you offered has expired.
Would you mind uploading it again?
Thank you very much.
Erica
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Thomas Yeo