you can try a modification of the method that I just sent out. In this case you are dealing with surface ROIs, so
Use mri_annotation2label to create labels of each annotation, then mri_label2label --srclabel ./your.label --srcsubject fsaverage --trgsubject talairach --regmethod volume --trglabel your.mni305.label There will be an entry for each voxel in the label. The coorrdinates in your.mni305.label will be in mni305 space. doug On 11/08/2015 10:03 AM, André Schmidt wrote: > Hi Bruce > > Thanks for your help. This is what I have done: > > - I used recon-all to define 84 brain regions. > - I ran tractography with these 84 regions as seeds. > - Then I used network-based statistics to compared the obtained connectivity > matrices (84 x 84) between two groups. To visualize the output, I need a txt > file including the MNI coordinates of each node. > > Please find attached my seed/node list. I simply need the x, y and z value > for each node. > > Many thanks for your help, much appreciated. > André > > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce > Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: Sonntag, 8. November 2015 15:45 > An: Freesurfer support list > Betreff: Re: [Freesurfer] node coordinates > > Hi Andre > > are you going to do a group analysis afterwards, or so you just want the > node coords? The fsaverage subject is already in MNI coords so you can > transform to it I believe (Doug can confirm). > cheers > Bruce > > > On > Sun, 8 Nov 2015, André Schmidt wrote: > >> Hi Bruce, >> >> Thanks for your reply. But where can I find the node coords? So far I only >> have names for the nodes. I guess the second step would then be to transform >> them from Talairach to MNI. >> >> Thanks again. >> Andre >> >> ________________________________________ >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce >> Fischl [fis...@nmr.mgh.harvard.edu] >> Gesendet: Samstag, 7. November 2015 17:30 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] node coordinates >> >> Hi Andre >> >> You can apply the transform in the talairach.xfm to the node coords. Not >> sure if we have anything to do this by default - Doug would know >> >> cheers >> Bruce >> >> On Sat, 7 Nov 2015, >> André Schmidt wrote: >> >>> Dear experts, >>> >>> I defined 84 regions obtained from the aparc+aseg.mgz file as my nodes for >>> later graph analysis. For visualization purposes, I want to assign each node >>> the corresponding MNI coordinates. Can you please help me how I can do this? >>> Is this documented somewhere? >>> >>> Many thanks for your help >>> André >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
