Hi Lorenzo,
The hippocampal subfield segmentation routines are only available from FreeSurfer 5.1, so you'll need that version to run the code.
If all your data is already pre-processed with an older version of FreeSurfer, you might be able to simply run the hippocampal subfield segmentation routines only using 5.1, although your version (4.3.0) sounds very old (and therefore might not produce the correct output files needed by the hippocampal subfield stuff). The safest is to re-analyze everything from scratch using 5.1.
Hope this helps,
Koen
On Wed, Jul 4, 2012 at 10:43 AM, lorenzo pasquini lollopasquini@yahoo.it wrote:
Dear Freesurfer experts,
I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command:
recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files aseg.mgz, nu.mgz, talairach.xfm
Does this error occur because I am using an old Freesurfer version? If this is the case which is the optimal version to run hippocampal segmentation? Should I process my whole data again with the newest version? Unfortunately I did not find any convincing answer from the posting list where I had the impression that version 5.1 is facing some problems regarding hippocampal segmentation. Thank you very much and kind regards,
Lorenzo Pasquini
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