I am trying to run the first recon-all command on Seimens dicom files to convert to mgz. I moved the files for each acquisition to a separate directory ex: 001 002 003, 3 subdirectories each containing the files for each scan acquisition.
I then run the command recon-all -i 447-5-440.ima -i 447-6-568.ima -i 447-4-312.ima -s 030217_vc11174
-where 447-5-440.ima, 447-6-568.ima, and 447-4-312.ima are the first files that appear in each acquisition directory.
The error I get is "cannot find 447-5-440.ima".
Any help would be greatly appreciated. Do I need to run this command from the directory where the files are located? Do I need to set my SUBJECTS_DIR each time to the individual session?
Thank you. Lindsay Casmaer Washington University in St. Louis lcasmaer@artsci.wustl.edu