Hi Doug, I've run recon-all -all. I ended up inputing an .mgz file converted from a .nii file that was converted from a .dicom. Was needed info lost somewhere along the way?
Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does one need -anat?)successfully, because it generated the following folders: bem, label, mri, scripts, src, stats, surf, tmp, touch, trash. And the bem, src, and trash folders are empty, but the others are full of files. Eek. -Michelle > 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 _______________________________________________ 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.
