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

 

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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

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