Hi Doug, Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program is? I had done this:
setenv SUBJECTS_DIR /home/fsl/structural So this SUBJECTS_DIR is not located where FreeSurfer is.
Is the following the exact correct path: FreeSurfer/$SUBJECTS_DIR/LD08/subjectname where LD08 is the file subjectname says LD08 and freesurfer must be capitalized as FreeSurfer?
and all the retinotopy data can be in: /home/fsl/structural/bold
and recon-all subfolders and data in /home/fsl/structural
Sorry for such a basic question.
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug
Michelle Umali wrote:
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message:
Session: /home/fsl/structural/LD08 ---------------- Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural
I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case.
Any help would be most appreciated. I am attaching the output, in case it is helpful.
Thanks. Michelle