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 > > >>> >>> ing Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>> >>>> I don't have a formal manual yet (working on it). Below are a list of >>>> steps that you need to run. The version 5 retinotopy stream is now >>>> integrated with the rest of FSFAST, which is documented here: >>>> http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt >>>> >>>> doug >>>> >>>> 1. Create retinotopy paradigm file in each run directory, eg, >>>> session/bold/001/rtopy.par >>>> session/bold/002/rtopy.par etc >>>> >>>> This text file identifies the data in the directory in terms of the >>>> stimulus type (polar or eccen) and the direction (pos or neg). Its >>>> contents should look somethign like: >>>> >>>> stimtype polar >>>> direction pos >>>> >>>> 2. Run preprocessing >>>> >>>> preproc-sess -surface self lhrh -fwhm 5 >>>> >>>> 3. Create analysis (30 sec period, 'rtopy.par' is the name of the >>>> paradigm file from above): >>>> >>>> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ >>>> -retinotopy 30 -paradigm rtopy.par >>>> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ >>>> -retinotopy 30 -paradigm rtopy.par >>>> >>>> 4. Run analysis >>>> >>>> selxavg3-sess -a rtopy.self.lh -sf ... >>>> selxavg3-sess -a rtopy.self.rh -sf ... >>>> fieldsign-sess -a rtopy.self.lh -occip -sf ... >>>> fieldsign-sess -a rtopy.self.rh -occip -sf ... >>>> >>>> 5. View results >>>> a. Significance maps: >>>> tksurfer-sess -a rtopy.self.lh -s sessid >>>> b. Display raw angle >>>> tksurfer-sess -a rtopy.self.lh -s sessid -map angle >>>> c. Display angle masked by by sig >>>> tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked >>>> d. Display field sign >>>> tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
