[MINC-users] Freesurfer

[Trisanna Sprung-Much]

Thanks Mishkin,

I haven't had much luck with posting questions so was hoping I could meet
with someone in person at the MNI:

Specifically - I have labels that have been painted on the T1 volumes of
several ICBM brains in Display. While I am going to be generating some
probability maps using this data in MNI space, I would like to generate
surfaces for the brains in Freesurfer (which I am in the process of doing)
and generate probability maps using a surface-based registration, as I
think the maps would be much more accurate.

I have been told to use the *mrivol2surf command *to put the labels onto
the Freesurfer surfaces, but need a .dat file containing information about
the registration matrix to run this command:

mri_vol2surf [<options>] --src inputfile --out outpufile --srcreg
registrationfile --hemi hemisphere

I do not have any dat files when I run recon-all and so was told to
generate the dat files using *mri152reg*. However, most of my ICBM brains
are registered to the MNI305 template and so my labels are in this space.
The mri152reg would only work for the 5 brains that I have that are
registered to ICBM152 nonlinear template. (Essentially, these brains were
passed on to me from another student and so are registered to various
templates)

*To start, any idea how to get the labels.mnc onto my Freesurfer surfaces?*

thanks so much,

Trisanna



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


On Tue, Apr 12, 2016 at 3:56 PM, Mishkin Derakhshan <mishkind at gmail.com>
wrote:

> Hi Trisanna,
> Best to actually post your question. I have a bit of experience but it
> is from 5 years ago now, so using FreeSurfer v4.5 and v5.0.
> mishkin
>
>
> On Tue, Apr 12, 2016 at 7:06 AM, Trisanna Sprung-Much
> <trisanna.sprung-much at mail.mcgill.ca> wrote:
> > Hello
> >
> > I am a graduate student in the lab of Michael Petrides and I am curious
> as
> > to whether anyone has a decent amount of knowledge about Freesurfer. I
> have
> > been slowly learning how to use it, using the youtube videos and wiki
> page
> > available, and also the email list. However, I have a specific question
> > regarding some labels I have created in Display and the email list has
> not
> > been successful.
> >
> > Any help would be greatly appreciated!
> >
> > best wishes
> >
> > Trisanna Sprung-Much
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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