Dear FreeSurfer Developers,
I am attempting to run recon-all on 7T MP2RAGE images (resolution 0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³.
I used the data directly from the scanner (without reorientation to standard etc.) and used the following command:
recon-all -s $subject.freesurfer -hires -i $subject.mp2rage.nii -expert /media/NeuroMet_Project/scripts/expert.opts -all -hippo-subfields"
As expert option I used only: mris_inflate -n 15
The processing starts fine but ends with the following error:
ERROR: dimension mismatch between input volume and seg input 321 321 321 seg 322 322 322
Could you please help me dealing with this problem? I attached also the log-file
Thank you so much.
Best Theresa
------------------------------------------------------------------------- Charité – Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC Dipl.-Biol. Theresa Köbe AG Kognitive Neurologie Wiss. Mitarbeiter Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2 http://www.charite.de/service/lageplan/plan/map/ccm_sauerbruchweg_5/<redir.aspx?REF=mc29RH9tIXK9qgoNB0UJ6dmsQ-pCBih_Q7so140WG76sl9oBFOLTCAFodHRwOi8vd3d3LmNoYXJpdGUuZGUvc2VydmljZS9sYWdlcGxhbi9wbGFuL21hcC9jY21fc2F1ZXJicnVjaHdlZ181Lw..>