I can answer the first question. The brain, T1 and filled folders will remain empty if you ran recon-all using .mgz files in your orig folders. If you were using COR formatted files, then the brain, T1 and filled folders would contain COR files following recon-all completion.

Using .mgz files is the recommended approach, so you are fine having empty brain, T1 and filled folders. The folders exist for compatibility with installations using COR formatted files.

On Thu, 2005-09-22 at 11:35 -0500, Clifford A. Smith, PhD wrote:

First, I have successfully completed recon-all on my Mac. I created the subject directories using mksubjdirs prior to running recon-all. After running recon-all the files are all in the mri folder, and the respective folders (eg brain, T1, and filled) remain empty. Is it necessary to build the folders?

Second, I would like to use the dti feature in tkmedit. I have the vector and fa volumes calculated with several computer packages in Analyze format. What does tkmedit need to read? A 4d volume with the three vector volumes plus the FA volume?

Thanks.

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Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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