Creating functional ROI - Freesurfer

11 Nov 2017

Hi Doug,

I ran the funcroi-config command the same way the tutorial
suggested: *"funcroi-config -annot aparc fusiform -analysis
eba-fba.native.rh -contrast faces-vs-objects -thresh 2 -sign pos
-roi rh.fus.test.roicfg -force"*

However, I got this error:
*"annotations can only be used with surface-based analyses"*
I have done my mkanalysis-sess in the _native space_, i.e.:
*"**mkanalysis-sess -fsd bold -stc odd -surface self rh -fwhm 5
-event-related -paradigm ..."*

Do you think this is the problem? Meaning, the surface here should
be fsaverage instead of self? And if yes, what if I need
everything in the native space?
Thank you,

Ashley

    On Mon, Nov 13, 2017 at 10:21 AM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
    wrote:

        Start with funcroi-config. Run it with -help to get
        documentation
        including several examples. Let me know if you still have
        questions

        On 11/11/2017 11:56 AM, Ashley Cole wrote:
        > Dear Doug/Bruce,
        > I appreciate any insights on this.
        > Thank you,
        > Ashely
        >
        > ------------------------------------
        >
        >
        > I am new to FreeSurfer and I apologize in advance if my
        questions are
        > too naiive.
        >
        > My main goal is to keep everything in the native space.
        Also, I am
        > looking for percent signal change in selected ROIs.
        >
        >
        > First, I ran recon-all command. Then, I preprocessed the
        functional
        > data in native space. The command that I ran was:
        >
        > preproc-sess -s sess01 -fsd bold -stc odd -surface self
        lhrh -mni305
        > -fwhm 5 -per-session -force
        >
        >
        >
        > Then, I configured my analyses and contrasts in each
        hemisphere, as
        > well as the volume.
        >
        > Finally, I ran the analyses for each hemispheres and the
        volume. I ran
        > this command:
        >
        >
        > selxavg3-sess -s sess01 -analysis ffa.native.rh
        >
        >
        >
        > Lastly, I visualized the results by running these commands:
        >
        > tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c
        > faces-vs-bodies -self
        >
        >
        >
        > tkmedit-sess -s sess01 -analysis ffa.native.mni -c
        faces-vs-bodies -self
        >
        >
        >
        > So far, I think I have done everything correctly. I am
        seeing the
        > activation ROIs where I am supposed to.
        >
        >
        >
        > Now, I would like to be able to select these
        ROIs/clusters, take their
        > voxel coordinates/numbers and create a mask. (These are
        my localizer
        > nii files.) Then, use this mask on the main experiment
        (non localizer)
        > nii files and get the percent signal change in those
        selected voxels.
        > Is this possible?
        >
        >
        > I have found this tutorial
        > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
        <https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs>
        > <https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
        <https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs>> but
        > unfortunately I am not following it. I don't see these
        options in
        > tksurfer.
        >
        >
        > Also is it possible to create an ROI on the surface?
        >
        >
        > I appreciate any help.
        >
        >
        >
        > Thank you so much
        >
        >
        >
        > Ashley Cole
        >
        >
        >
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        --
        Douglas N. Greve, Ph.D.
        MGH-NMR Center
        greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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        Fax: 617-726-7422 <tel:617-726-7422>

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