HI doug, thanks for getting back to me. I was able to solve the problem on my own.

thanks again Jon ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, July 31, 2014 4:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg

Are you sure you are using orig.mgz when you run mri_vol2vol and not something like rawavg.mgz? You don't need to spec orig.mgz explicitly (it will use that by default)

doug

On 07/21/2014 04:51 PM, Jon Wieser wrote:

hi freesurfer experts

I am compiling the FA segment stats for several subject

I used mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp nearest --o fa.anat.mgh

then I used:

mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stats

for some of my subjects, Iam getting the following error:

mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser UseRobust 0 Loading mri/wmparc.mgz Loading dti/fa.anat.mgh ERROR: dimension mismatch between input volume and seg input 256 256 192 seg 256 256 256

can you tell me how to fix this?

thanks Jon

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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