Hi Prof,
Thanks for the speedy reply,
When you specify fsaverage5 as -srcsubject and your own subject as -trgsubject, the code executes but the resulting .annot file looks like a mess.
Your proposed two-step call to mri_surf2surf seems more promising. If I run the following:
mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh --sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval ./lh.YeoUpsample.annot
I end up with a .annot file in the same space as fsaverage, but there seem to be large gaps between the labels. Here's a screenshot of what I mean:
Do you have any suggestions on how to account for this? Is there some unresolved mismatch between the number of vertices following upsampling, perhaps?
Best wishes,
Richard
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.par...@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
Hi Richard,
This occurs because the gaps exist in the original fsaverage5 split_component parcellation. As explained in the documentation text file (Yeo_JNeurophysiol11_SplitLabels_README which should also be included in the zip file), one of the steps taken to generate *.split_components.annot involved removing vertices at the boundaries between parcels. This is to reduce the mixing of signals across parcels, e.g., due to spatial smoothing.
You can see these gaps if you plot the fsaverage5 annot on the fsaverage5 subject. Therefore when the parcellation is upsampled from fsaverage5 to fsaverage, the gaps are propagated. I admit the gaps do not look very visually pleasing because going from fsaverage5 to fsaverage involved an upsampling factor of 4. However, I think the gaps should not be detrimental to your analysis.
How does the parcellation look when you transfer the (upsampled) fsaverage parcellation to the individual subject's surface?
Regards, Thomas
On Mon, Dec 14, 2015 at 6:43 PM, Parker, Richard richard.r.parker@kcl.ac.uk wrote:
Hi Prof,
Thanks for the speedy reply,
When you specify fsaverage5 as -srcsubject and your own subject as -trgsubject, the code executes but the resulting .annot file looks like a mess.
Your proposed two-step call to mri_surf2surf seems more promising. If I run the following:
mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh --sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval ./lh.YeoUpsample.annot
I end up with a .annot file in the same space as fsaverage, but there seem to be large gaps between the labels. Here's a screenshot of what I mean:
Do you have any suggestions on how to account for this? Is there some unresolved mismatch between the number of vertices following upsampling, perhaps?
Best wishes,
Richard
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.par...@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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