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 Greve<gr...@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 >>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
