Hi Michelle

many of the FS binaries use knowledge of the standard directory tree under SUBJECTS_DIR to do things like lookup the original coordinates of a flattened or inflated vertex, which is why you need the --s and --lh.

cheers Bruce On Thu, 13 Oct 2011, Michelle Umali wrote:

Dear Freesurfers, I know this is a very simple question.  I'm just having trouble specifying the correct directories for rtview based on the example. When I run rtview, it can't find the image files that really do exist in the directory.

For the following example in the help section: I did what I thought were the proper replacements

Example: cd sess/bold/rtopy.lh  rtview --s subject --lh --eccen \    --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii

What I did: cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh rtview --s sj07 --lh --eccen  \    --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii

Then I tried getting rid of the --s and --lh flags because I was already in that directory, but that didn't help either.

If I'm already in the in the correct folder why do I still have to specify --s and --lh?

Thanks. Michelle