Try something like mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.yeo.stats -b -a ../label/lh.yeo.annot -c ../label/yeo.annot.ctab 1040 lh white
Assuming that your yeo atlas is in $SUBJECTS_DIR/$subject/label/lh.yeo.annot
On 7/15/2020 2:05 PM, Martin Juneja wrote:
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Dear Doug,
Thanks for your response !
Yes, I have Yeo atlas in the individual space, and recon-all.log has the following command:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 1040 lh white \n computing statistics for each annotation in ../label/lh.aparc.annot.
Could you please help me in customizing this because it seems it gives me stats for each annotation e.g. stats for 34 areas (for Desikan atlas) and 7 networks (for Yeo 7 network, I think this is averaged over each network, correct?), but I am looking for stats of the regions which constitute those networks (e.g. stats for the areas which are part of the default mode network i.e., 4 individual stats of 4 individual red colored regions in the following figure).
DMN.png
On Wed, Jul 15, 2020 at 8:54 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
If you have the Yeo atlas in the individual space, you can use mris_anatomical_stats to compute stats the same as in the Desikan atlas. Look in recon-all.log for the command line and customize it as needed On 7/14/2020 5:00 PM, Martin Juneja wrote:External Email - Use Caution Hi experts, I extracted network-wise cortical measures (i.e., 7 cortical thickness values for 7 networks for Yeo atlas). I was wondering if there is a way to get the cortical thickness of each ROI within each of these networks e.g., cortical thickness values of all the ROIs which constitute default-mode network of Yeo's 7 network parcellation, and then cortical thickness values of all the ROIs which constitute limbic network of Yeo's 7 network parcellation, and so on. I know Desikan atlas can be used to get morphometry measures of 34 ROIs per hemisphere. But the problem is that e.g., default-mode ROIs from Desikan atlas do not completely overlap with the DMN of 7-network parcellation from Yeo atlas. In other words, superior frontal cortex from default-mode network of Yeo 7 network parcellation is a big chunk compared to several small ROIs (some partial and some full) in Desikan atlas, so I do not see any way how to find ROIs which just match with that superior frontal cortex of default-mode of Yeo's 7 network. Any help would be much appreciated ! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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