Good Morning

Let me start on a positive note by saying I think I'm making headway!

So, I am trying to find someone who might be around to help me with the FreeSurfer stuff...but in the meantime I am going to try to generate an AFNI dataset from the coordinates from my label files (ignoring the first column that is the node index). Looking over some of the previous postings there was mention of 3dSurf2Vol to do this. --Maybe this will solve the problem that I am getting with the node index from mri_label2label, but I'm not getting my hopes up!--

The posting I have referred to is pasted below. The 3dSurf2Vol command I have tried to use is this:
3dSurf2Vol \
-surf_A wm \
-surf_B pial \
-surf_xyz_1D rh.IT.1D'[1-3]' \
-grid_parent SurfVol_Alnd_Exp+orig \
-map_func mask \
-prefix rh.IT

What I'm finding is what appears to be the right SHAPE for the label file. It is no longer a series of random speckles....BUT it's location is wrong. (for example, something that should be right IT is coming up in the left prefrontal cortex). It's hard to be completely sure, but I think it's the right shape for what WOULD be IT if it were superimposed on that part of the structural brain.

Any ideas?

As Always --much appreciation
Jennine

********previous posting********************

If your only goal is to map these coordinates to a volume,
you might just try:

3dSurf2Vol -surf_xyz_1D MY_COORDS.1D'[1-3]' \
-grid_parent AFNI_DSET+orig \
-map_func mask
-prefix SURF_DSET

Here, MY_COORDS.1D is your coordinate file. Columns 0 and
4 are ignored, and 1-3 hold the coordinates. SURF_DSET is
whatever prefix you want for your AFNI dataset.

For more information on this, see "3dSurf2Vol -help",
example #4. Note that you need version 3.4 for this, as I
had trashed the -surf_xyz_1D option in version 3.0.

Please let me know how it goes.

- rick