Hi again, so I did use the -cm flag to conform the voxels to its minimum size of .8mm iso (which is also the native size of my data set) during the mri_convert process and used the -noconform flag for the mri_normalize stage during autorecon1 to prevent further conformation to 1mm.
But now recon-all exits with an error at stage 12 (http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). The error message I got is as follows: #-------------------------------------------- #...@# Intensity Normalization2 Wed Mar 11 08:38:44 CET 2009 /home/falk/freesurfer/subjects/claus/mri mri_normalize -f home/falk/freesurfer/subjects/claus/tmp/control.dat -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /home/falk/freesurfer/subjects/claus/tmp/control.dat... not interpolating and embedding volume to be 256^3... 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... Linux xxxxxx 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Mar 11 08:38:55 CET 2009 --------------------------------------------- Does anyone know what to do? Regards, Falk -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, March 06, 2009 1:26 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel size smaller than 1x1x1mm? Hi Falk, yes, you can use the "conform to min" (-cm I think) switch in recon-all. Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard for whole brain morphometry because of dielectric effects. Good luck. Bruce On Fri, 6 Mar 2009, Falk Lüsebrink wrote: > Hi Freesurfers, > > I'm currently doing my bachelors thesis in medical engineering and I'm > trying to measure the cortical thickness of scans acquired by a 7T MRT. > > A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that > high resolution scans with a voxel size smaller than 1x1x1mm (like > .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of autorecon > - I think during the mri_convert process. > > Is it possible to keep the native size or does Freesurfer need to change the > voxel size to 1mm in order to do the segmentation correctly? > > Regards, > Falk > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
