Hi Michelle,
the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg
recon-all -all -subject LD08-anat -i anatomical.dicom
this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have not done this, you should do this first. Look at the wiki for how to run the anatomical analysis.
Once this is done, you should unpack your functional data (looks like you might have done this already). In the session directory, create a text file called "subjectname". Put the subject name (ie, LD08-anat) into the subjectname file.
doug
On 4/5/11 2:15 PM, Michelle Umali wrote:
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 Grevegreve@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
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