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:fischl@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

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