On 04/27/2016 10:24 AM, Martin Juneja wrote:

Dear FreeSurfer experts,

I am using FsFast functional connectivity walkthrough steps to analyze fMRI data from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...

I am able to run all these steps successfully and can view the voxel-wise distribution maps.

I was wondering if it's possible to: (1). overlay externally defined ROIs (e.g. R1.nii) on these maps e.g. on pcc (partial correlation coefficient) to find the correlation coefficient between R1.nii and seed region, may be averaged over voxels or voxel-wise?

Are you trying to just overlay R1 onto the results or do you want to use R1 as a seed? If as a seed, then you need to create a binary mask in the anatomical space, eg, $SUBJECTS_DIR/subject/mri/R1.mgz, then specify -seg R1.mgz -segid 1 when running fcseed-config.

(2). display labels (name of the areas) as well on the distribution maps?

It this is in the volume, then you can create a lookup table (similar to $FREESURFER_HOME//FreeSurferColorLUT.txt with the name of your label, then load both as a segmentation. If this is on the surface, then you need to map R1 to the surface (probably mri_vol2surf), then convert to a label (mri_cor2label with --surf option), then convert the label to an annotation (mris_label2annot)

Any help would be really appreciated.

Regards, MJ

---

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