Hi Doug,

I am running Freesurfer on MacOsX Darwin. The command
as you suggested:
mri_vol2vol --targ rawavg.mgz --mov orig.mgz --reg
reg.dat --o orig-in-rawavg.mgz

using the mri_vol2vol version that came with FS I get
the message: ERROR: Option --targ unknown

using the mri_vol2vol from the link you provided
results in: Exec format error. Binary file not
executable.
Probably, that is a version compiled for x86 and not
Mac?

Thanks for your help,
Frederick





--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

  

This should do it:

tkregister2  --targ rawavg.mgz --mov orig.mgz --reg
reg.dat --noedit
mri_vol2vol --targ rawavg.mgz --mov orig.mgz --reg
reg.dat --o 
orig-in-rawavg.mgz

If this does not work with your version of vol2vol,
then use the one here:


    

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
  

Frederick Klauschen wrote:

    

Hi,

I have to bring up an issue again which we had some
discussion about before, but which we haven't yet
found
a satisfying solution. I would like pose my
      

question a
    

little more precisely again:
1) I have a dataset that is in 181x217x181
coordinates.
2) I am processing it as follows:
  >  mri_convert name.img  name/mri/orig/001.mgz
  >  recon-all -motioncor -subjid name
3) after step 2, the resulting dataset is somehow
transformed to a 256x256x256 dataset, i. e. the
181x217x181 is embedded into the 256^3 array:
it is rotated and the origin in 181x217x181 is not
      

the
    

origin in the 256x256x256 array.
4) Since I would like to do a voxelwise comparison
between the recon-all result and my initial dataset
1),
I need to backtransform the result into the
181x217x181 coordinates (and of course, the
backtransformation should be the exact inverse of
      

the
    

transformation in 2). I haven't found any info
      

about
    

how this transformation is done by FS, mri_info
      

does
    

not provide it.

Thanks,
Frederick

 



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

In order to help us help you, please follow the
steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



    

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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting