Hi Michele,

this means that the computed talairach transformation was deemed to be unlikely and therefore possibly wrong. This usually occurs when the input volume is in the incorrect orientation. Did you convert to analyze format at any time? If you bring the orig.mgz up in tkmedit are the orientations correct? That is, does the sagittal view look sagittal, etc...? It's also possible that the tal is correct but the suject was in an unusal orientaton. If you visually inspect the tal and it's correct and the orientation are correct, then use the -notal-check flag to skip checking.

cheers Bruce

On Tue, 29 Jun 2010, Michele Placci wrote:

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, NIFTI format (converted from DICOM) to calculate brain volume.

I ran

recon-all -autorecon1 -autorecon2 -subjid <..."file with extension.mgz, after the conversion with mri_convert from a unique file .nii" >

and I obtained the errors that you can see in the attachments.

Any suggestion?

Thank you in advance. Michele.