Re: [Freesurfer] extracting hand drawn ROIs to Afni space

Hi Paul, do you still have a problem that needs to be solved? doug

On 02/18/2013 04:39 PM, Paul Beach wrote:

Thank you for forwarding this.

I realize I need to further clarify my issue as well.

With the help of Doug Greve I've taken hand made ROIs in tksurfer, repackaged them into a new annotation, and repackaged that into a new aseg file for an average subject. Now (and this is where I'm stuck) I'm trying to take those newly minted ROIs, place them onto individual subjects' brains and THEN send them to Afni for each of those subjects (before doing seed correlation analysis).

Previously I had been using mri_label2label to place the averaged subject ROI into single subjects' folders and then mri_label2vol to get them ready to send to Afni. However, this method was not producing ROIs that covered the extent of a region's gray matter. Thus, Doug's solution of re-annotating and re-segmenting.

Hopefully that makes things a bit easier.

Thanks again for your help! Paul

On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Paul

we usually call those labels and have an ascii label file format.
Not sure how to get that into AFNI, but I'm zure Ziad (ccd) knows.

cheers
Bruce

On Mon, 18 Feb 2013, Paul Beach wrote:

    Hi there,
    Through the help of the Freesurfer Q&A staff I've been able to
    get ROIs
    drawn in tksurfer into an augmented aparc+aseg file of an
    averaged subject.
    I need to be able to get those ROIs, which are not part of the
    color LUT,
    into Afni space.

    For ROIs that are already in the LUT, getting them to Afni is
    no problem, I
    simply use a 3dcalc command. However, I have the problem of
    needing to
    export newly parcellated and segmented ROIs that aren't in the
    Freesurfer
    LUT to Afni space.

    Is there a way to do this short of creating a new "spot" for
    them in our
    LUT? If not, how does one go about adding ROIs to the LUT
    and/or creating a
    LUT specific to my needs (since the Wiki suggests not fussing
    with the
    original LUT)?


    Thanks,
    Paul
    --





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-- Paul Beach DO/PhD candidate - Year V Michigan State University

• College of Osteopathic Medicine - OMS V
• Neuroscience Program
  • Bozoki Lab: Neurology/Radiology
• President: American Physician Scientist Association, MSU COM Chapter

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