[MINC-users] Freesurfer

[Mishkin Derakhshan]

I'm afraid I don't have the specific answers to your mri_vol2surf
questions but maybe this will help.

When I did my analyses, I took the freesurfer surfaces and transformed
them into my native mnc space (i.e., the space where your input
T1.mnc.gz is in which should be the same as your labels.mnc).

The key transformation, (really just a translation) that I needed was:
    ${cras} = `mri_info --cras T1.mnc`;
    chomp(${cras});
    &cmd("param2xfm -translation ${cras} fs-to-minc.xfm");

And then I would apply that trasnformation to the freesurfer object to
get that object into my native mnc space.

Following that logic, all you might need to do is:
    ${cras} = `mri_info --cras T1.mnc`;
    chomp(${cras});
    &cmd("param2xfm -translation ${cras} fs-to-minc.xfm");
    &cmd("xfminvert fs-to-minc.xfm minc-to-fs.xfm");

And then minc-to-fs.xfm would be the transformation to take you from
your native minc space into your native freesurfer space (i.e., the
same space as your T1.mgz file).
If the freesurfer tools don't accept a .xfm file, it shouldn't be hard
to create a .dat file using the data in the .xfm.

hth,
mishkin


On Tue, Apr 12, 2016 at 10:30 AM, Trisanna Sprung-Much
<trisanna.sprung-much at mail.mcgill.ca> wrote:
> 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
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users