ziad Wrote:
-------------------------------------------------------
> chxc123 Wrote:
> --------------------------------------------------
> -----
> > I tried it and loaded the output file onto a
> > inflated std.141 surface. It looked like a mesh
> > covering the brain surface, but the locations
> and
> > size of BA areas looked fine.
> >
> Do you mean the color pattern covered the whole
> surface? What are the values at the regions
> outside of BAs when you right click on them in
> SUMA?
>

I tried to attach a figure to show this but it didn't work. I think it can be repeated with the following commands:

#hemi=lh or rh
#fsfolder: the folder with ${hemi}.BA.thresh.annot
#run it in the same subject's SUMA folder

FSread_annot \
-input ${fsfolder}/${hemi}.BA.thresh.annot \
-roi_1D ${hemi}.BA.thresh.annot.1D.roi \
-FScmap ${fsfolder}/BA.thresh.ctab \
-dset ${hemi}.BA.thresh.annot.niml.dset \
-cmap_1D ${hemi}.BA.thresh.annot.1D.cmap

SurfToSurf \
-i_fs std.141.${hemi}.smoothwm.asc \
-i_fs ${hemi}.smoothwm.asc \
-prefix temp.141. \
-mapfile std.141.${sbjname}_${hemi}.niml.M2M \
-dset ${hemi}.BA.thresh.annot.niml.dset

Then load the temp.141.${hemi}.BA.thresh.annot.niml.dset onto an inflated std.141 surface to see the result.

Thanks,
Xiangchuan