Stupid me!

I just found what I need: mri_cor2label. It does exactly what I want:

"A utility to sample a volume onto the surface, then create a label of all super-threshold points regardless of whether they are connected or not"

I failed to recognize that I would have to binarize my fMRI activations first using mri_binarize (and selecting an intensity threshold).

This binarized volume files then goes into mri_cor2label using "--id 1".

works perfectly.

Sorry for this. Bastian.

On 24 July 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Bastian

can you explain further what you would like? A utility to sample a volume onto the surface, then create a label of all super-threshold points regardless of whether they are connected or not?

cheers Bruce

On Thu, 24 Jul 2014, Bastian Cheng wrote:

...

Dear Freesurfer-Experts,

Is there an automated way to convert an overlay volume to a label file? I guess I would look for a command called "vol2label".

I am currently projecting volume files (fMRI activiation hotspots) to surfaces (mri_vol2surf): this works nicely.

However I then would have to define labels manually (using "custom fill") by clicking on all (unconnected) spots on my surface.

Please excuse any redundancies, I have not found a good solution in the forum yet.

Best regards, Bastian. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hi Xiaomin

how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) and you reran recon-all it should have preserved your edits, even though it regenerated the file. Have you checked?

Bruce

On Fri, 25 Jul 2014, Xiaomin Yue wrote:

Hi,

My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz.   I re-run the anlysis using recon-all -s cologna -autorecon2-wm.  From some reason, the analysis regenerated wm.mgz from brain.mgz, which of course replaced my edited wm.mgz.   Did I do some wrong here?

Thanks, Xiaomin