thanks, Doug. I am still extremely confused, however. Am I meant to run recon-all first? I was told in a previous email that I should do this first, however, I thought that Freesurfer takes the volumes and does a linear registration to MNI305 template, which would not work for my scans that are linearly registered to ICBM152 nonlinear 2006 template...

When you have a moment, could you please outline in a step by step manner the steps I should run to take my labels.mnc and my volumes such that I can generate surfaces for those 50 volumes, overlay the labels (for which I thought I was using mri_vol2surf) and then edit those labels to make them more accurate? The idea is that I want to generate some sulcal probability maps using surface-based registration, as I can already generate probability maps using volumetric registration quite easily.

many thanks

Trisanna

Ph.D. Candidate

McGill University

Integrated Program in Neuroscience

Psychology

On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

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> 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> 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
>
>
>
>
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