You should check that anatomical analysis and make sure that it is correct. Once that is done, make sure that the subjectname in the subjectname file is correct, then preproc-sess should run.
doug
Michelle Umali wrote:
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