You actually need the ROI in the anatomical volume space (ie, the "conformed" space of 1mm3, 256^3). If you have a binary (ie, 0,1) mask of your ROI called roi.mgz, then use -seg roi.mgz -segid 1

On 04/28/2016 08:22 PM, Martin Juneja wrote:

Hi all,

I am trying to perform step-3 from the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...

But I do not have segid because the LookUp table FreeSurfer creates after running recon-all doesn't have the area I am interested in. So I defined the ROI externally, converted it into surface using vol2surf and further into .label file using cor2label.

I was wondering how can I use this externally created ROI (either in vol format, or surface format or label format) in this command: fcseed-config.

I made sure that the external ROI is perfectly aligned where it was supposed to be.

Thanks. MJ

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer