no, it would be more like a talairach alignment On Wed, 24 Jul 2013, Mark Plantz wrote:

Hi Bruce, Thanks for the reply. Would 'bbregister' work to register the files to eachother or would there be a more useful way to do that?

Also I noticed that across many of the subjects there is a slight difference in the TR, TE, TI, and flip angle values.

For instance, one of the subjects has a TR: 9.39 and another might have a TR: 9.44. This clearly prevents me from using them to create an atlas. I am not really sure why these values are slightly off, they should be the same. Is there anyway to change those values manually? Is it because I am using the T1.mgz files?

Thank you!

• MP

On Tue, Jul 23, 2013 at 3:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mark

  have you tried using  a transform? Usually with more than one subject we require that
  they be registered. I haven't looked at that code in a long time, so I am not positive
  that it would fix this problem, but it might. In any case if they aren't registered it
  won't generate a useful atlas, even if it does run to completion
  Bruce

  On Tue, 23 Jul 2013, Mark Plantz wrote:

        Hello freesurfers,
            I recently ran into a problem with mri_ca_train, a function that creates
        a .gca atlas from a manually segmented volume and input volume(s). 

          My command line is:

        mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca

        The results:

        processing subject CMH-11461, 1 of 1...
           reading input 0:
        /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/norm.mgz
        filling holes in the GCA...
        404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled)
        computing covariances for subject CMH-11461, 1 of 1...
        average std = 6.1   using min determinant for regularization = 3.7
        298584 singular and 4268 ill-conditioned covariance matrices regularized
        writing trained GCA to /Users/IngvalsonLab/Desktop/atlas1.gca...
        classifier array training took 0 minutes and 27 seconds.
        dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 
        dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 
        dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz
        CMH-11460 CMH-11461 ~/Desktop/atlas1.gca 
        reading T1 data from subject's mri/T1.mgz directory
        training on 2 subject and writing results to
        /Users/IngvalsonLab/Desktop/atlas1.gca
        ***************************************************************************
        processing subject CMH-11460, 1 of 2...
           reading input 0:
        /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz
        ***************************************************************************
        processing subject CMH-11461, 2 of 2...
           reading input 0:
        /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/T1.mgz
        filling holes in the GCA...
        468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled)
        computing covariances for subject CMH-11460, 1 of 2...
        GCAupdateNodeCovariance(17, 35, 28, 4): could not find label
        dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 


           According to the fswiki, the same bug was eliminated in the 2009 version.
        For some odd reason, this command works with one subject, but not with
        multiple subjects.

        Any ideas?

        Thanks in advance,

        MP

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