Thanks Ziad Bruce

On Feb 19, 2013, at 10:42 PM, ziad ziad.ss@gmail.com wrote:

Hello Paul,

There are a couple of ways I can think of bringing the new ROIs to AFNI land from FreeSurfer. I can suggest the following, with the assumption that you seek to dump the average time series from single-subject data using an ROI defined on the FS average surface.

1- Get a list from FreeSurfer of the nodes indices that constitute the ROI on the FS average surface. That list can take the form of a dataset, that we'll call ROI_dset_avg. Use GFTI/NIFTI for surface/volume exchange format between FreeSurfer and AFNI. 2- Create a standard mesh version of the FS average surface, assuming you don't have one already. You can do that much as you would for a regular subject using @SUMA_Make_Spec_FS. 3- Use SurfToSurf, or MapIcosahedron to map the ROI_dset_avg from the original fsaverage surface mesh onto any of the standard-mesh versions of fsaverage. We'll call that dataset ROI_dset_avg_std. This new dataset can now be used on any of your subject's standardized meshes, as long as you use the same icosahedral mesh. 4- Create for each subject a volumetric mask of ROI_dset_avg_std with 3dSurf2Vol

I don't know how well you know how to use the SUMA tools I mentioned above, but if you need more detailed help let me know.

cheers, Ziad

On Feb 18, 2013, at 4:39 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 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

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