Dear colleagues,

We are recently using the freesurfer recon-all command

recon-all –s XXXX –I XXXX.nii.gz

recon-all –s XXXX –all

where XXXX stands for the subject ID. I have been trying to execute this command with the different input files:

1) original dicom-files

2) nii-file where the field of view was cut, apart from that the same file as in 3)

3) nii.gz-file, was computed by mri_convert with the files from 1)

We guessed results should be the same, but unfortunately, the segmentation looks slightly different in all three cases.

Maybe you can help us by trying to find out why the output files are different?

Thanks very much in advance!

Best regards,

Susanne

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Susanne Schell, Dipl.-Psych.

Sektion Störungen der Persönlichkeitsentwicklung

Klinik für Kinder- und Jugendpsychiatrie

Universitätsklinikum Heidelberg

Tel: (+49) – (0)6221-56 35135