what was your original input volume? What dimensions/voxel sizes and how did you convert it to .mgz in the first place? On Fri, 22 Aug 2008, vin wrote:
hi,
i am new to freesurfer. I tried reconstruction three times, autorecon1 works fine, but autorecon2 gives same error.
*recon-all -autorecon1 -subjid your_subject_name % worked fine. :)
**recon-all -autorecon2 -subjid your_subject_name* % this gives following error came in 11/ 12 hours.
error in mid anterior detected - correcting...
writing aseg with callosum to to /p/54/structural/t1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.5 minutes
cp aseg.auto.mgz aseg.mgz
#----------------------------- --------------- #@# Intensity Normalization2 Fri Aug 22 12:56:57 MEST 2008 /p/54/structural/t1/mri
*mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization reading from norm.mgz... mri_normalize: aseg volume aseg.mgz must be conformed using MR volume brainmask.mgz to mask input volume... unconformed source detected - conforming...* Linux xx.xxx.de http://buddha.neuro.rad.med.uni-tuebingen.de2.6.25.11-97.fc9.i686 #1 SMP Mon Jul 21 01:31:09 EDT 2008 i686 i686 i386 GNU/Linux
*recon-all exited with ERRORS at Fri Aug 22 12:57:18 MEST 2008
and that is how the directory looks like. [xx@xx mri]$ ls aseg.auto.mgz aseg.mgz brainmask.mgz norm.mgz nu_noneck.mgz orig.mgz T1.mgz talairach_with_skull.log aseg.auto_noCCseg.mgz brainmask.auto.mgz mri_nu_correct.mni.log nu.mgz orig rawavg.mgz talairach.log transforms
any one has any idea, where i am making mistake
Thank you very much / dhanyabad ji
vinod