You need to give it the full path to the file, eg 001/447-5-440.ima. I have a feeling that this will also fail because it's going to think that the .ima is the old siemens ima format. Let me know. Also, there's no need to put the dicoms in separate directories as freesurfer can find only those files in a dir that are part of the same series that you pass it.

doug

Lindsay Casmaer wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer