Re: [Freesurfer] mri_vol2surf after recon-all

For the 152, you can run mni152reg --s subject, then specify $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for the argument to --reg. I'll need to figure out how to generate a .dat/.lta for the 305.

On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:

Any ideas?

Trisanna

-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca mailto:trisanna.sprung-much@mail.mcgill.ca> wrote:

Hi Dr. Fischl

I have a mixture - some of the labels were painted in the MNI305
space (older ones) and the more recent ones are registered to the
ICBM152 nonlinear symmetric VI (2006) template.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
wrote:

    Hi Trisanna

    what space are your labels in?

    cheers
    Bruce
    On Tue, 5 Apr 2016, Trisanna Sprung-Much
    wrote:

    > Hi Freesurfer
    >
    > I have some labels (.mnc) that are painted voxels generated
    from a Montreal
    > Neurological Institute software. I am trying to project the
    labels onto the
    > surfaces generated from recon-all that I applied to the
    corresponding MRI
    > volumes.
    >
    > I used mri_vol2surf:
    >
    > mri_vol2surf --src labels.mnc --out test.mgz --srcreg
    talairach.auto.xfm
    > --hemi lh
    >
    > and got the following error:
    >
    > Error reading inplaneres from talairach.auto.xfm
    >
    >
    > Do I need a .dat file? If so, how can I attain it?
    Essentially, what is the
    > registration file that I am supposed to be using?
    >
    > Many thanks!
    >
    > Trisanna
    >
    > --
    > Ph.D. CandidateMcGill University
    > Integrated Program in Neuroscience
    > Psychology
    >
    >
    >
    >
    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


    The information in this e-mail is intended only for the person
    to whom it is
    addressed. If you believe this e-mail was sent to you in error
    and the e-mail
    contains patient information, please contact the Partners
    Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
    sent to you in error
    but does not contain patient information, please contact the
    sender and properly
    dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer