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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@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

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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@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