Re: [Freesurfer] Convert expert segmentation to FreeSurfer space

none of our tools use the nifti origin (and we don't have a way to set it). Do you need it for something else? FSL or SPM may have tools that can set it

On 03/07/2014 02:40 PM, Oualid Benkarim wrote:

I have a expert segmentation and i want to transform this file to GCA space. However, i first need to have the segmentation in conformed space cause the segmentation is 256x256x278 1mm and has a different origin. I tried the following:

...

...

mri_convert -rl orig.mgz -rt nearest mySeg.nii.gz

mySeg_conformed.nii.gz

The output mySeg_conformed.nii.gz has now 256x256x256 voxels, although has a different origin than GCA atlas

Is there a command to set the origin to GCA's?

Thanks

2014-03-03 17:35 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:

Hi Mohamed

the segmentations are in the individual subject "conformed" space.
The talairach.m3z is what is used to transform GCA to the
conformed coords

cheers
Bruce


On Mon, 3 Mar 2014, Mohamed Oualid Benkarim wrote:

    Hi all,

    I've performed FS subcortical segmentation and my purpose is
    to use these
    segmentations as seeds to another method.
    As FS uses GCA atlas to perform subcortical segmentation, I
    want to know if
    the aseg.mgz output is in GCA atlas space,
    or in original space except that the dimensions are
    256x256x256, 1mm.

    On the other hand, I also need to convert expert segmentations
    in native
    space to GCA atlas space, that is, the inverse
    of the process explained in
    http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat.
    I don't know
    if there is a command to do so,
    or we have to use a transformation matrix. In the latter case,
    FreeSurfer
    creates several tranformation matrices: talairach.lta,
    talairach.xfm, talairach.m3z....but it's is not clear which
    one I should
    use.

    Thank you in advance!!




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