Ryan,

Yes, you can use your old data with qdec. Just copy or link the 'fsaverage' subject to your SUBJECTS_DIR, and run recon-all -qcache -s <subj> on each subject. That maps your thickness data to the fsaverage surface at various smoothing levels, and is the primary input to qdec's mri_glmfit instantiation.

Nick

On Wed, 2008-11-19 at 13:12 -0500, Bruce Fischl wrote:

Hi Ryan,

if all you want to do is run qdec you can just run a very small part of recon-all (-qcache I think), then you should be all set. Nick can verify.

cheers, Bruce On Wed, 19 Nov 2008, Ryan Scotton wrote:

...

Hi Bruce,

My team has recently begun planning for data analysis after completing the overwhelming majority of our FreeSurfer runs and manual edits. However, it came to my attention that we do not currently have Qdec installed on our system...I realized that this is because we were using a very outdated version of FreeSurfer (3.0.4) that did not include Qdec. We have since downloaded the newest version so that we can begin data analysis, but this raises a bigger question: is it necessary for us to rerun FreeSurfer on all of our subjects (250+) if we are ONLY concerned with the white matter/grey matter surfaces and cortical thickness measurements? If not, spectacular. If so, is there only a small portion of the recon-all stream that we could run so that we could take care of this problem as fast as possible?

Thanks! Ryan

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