Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks,
Nathan
I don't think we have anything that will grow a mask on the surface. A slightly hacky way to do it would be to create a binary mask on the surface in which your seed vertex is 1 and all others 0 (you can do this on the cmd line with mri_volsynth with the following options --pdf delta --delta-crsf vertexno 0 0 0 0). You can then smooth it with mri_surf2surf. You can specify the number of dilations with the number of smoothing steps (--nsmooth-in), then use mri_binarize to threshold at some value just above 0 (eg, 10e-10).
doug
Nathan Dankner wrote:
Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hello,
i'm trying to take a label that i drew on each subject's surface into volumetric space so that i can extract fMRI parameters within this anatomically defined ROI. i am able to see the label within each subject's orig.mgz volume with tkmedit. however, i'm not sure how to convert this label file into a format that FSL will recognize, given that neither mri_surf2vol, not mri_convert recognize labels as valid input files.
any advice is most appreciated!
thanks, libby
Elizabeth O'Hare, Ph.D. Postdoctoral Fellow Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall, MC #3190 Berkeley, CA 94720 510-642-5554 edohare@berkeley.edu
Hey Libby, try using mri_label2vol. It will ask for a template volume and registration. If you are mapping it to each functional run use example_func as the template and the register.dat created by reg-feat2anat as the registration. If you are mapping it to a gfeat of the combined runs of each subject, then use the standard space (eg, avg152T1) as the template and the anat2std.register.dat from one of the functional runs (should not matter which one).
doug
On Tue, 1 Jun 2010, Elizabeth O'Hare wrote:
hello,
i'm trying to take a label that i drew on each subject's surface into volumetric space so that i can extract fMRI parameters within this anatomically defined ROI. i am able to see the label within each subject's orig.mgz volume with tkmedit. however, i'm not sure how to convert this label file into a format that FSL will recognize, given that neither mri_surf2vol, not mri_convert recognize labels as valid input files.
any advice is most appreciated!
thanks, libby
Elizabeth O'Hare, Ph.D. Postdoctoral Fellow Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall, MC #3190 Berkeley, CA 94720 510-642-5554 edohare@berkeley.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Elizabeth,
your best bet is probably to use mri_label2vol to write the label into a volume. I think it will take a registration file so you can write it out in functional coords
cheers Bruce On Tue, 1 Jun 2010, Elizabeth O'Hare wrote:
hello,
i'm trying to take a label that i drew on each subject's surface into volumetric space so that i can extract fMRI parameters within this anatomically defined ROI. i am able to see the label within each subject's orig.mgz volume with tkmedit. however, i'm not sure how to convert this label file into a format that FSL will recognize, given that neither mri_surf2vol, not mri_convert recognize labels as valid input files.
any advice is most appreciated!
thanks, libby
Elizabeth O'Hare, Ph.D. Postdoctoral Fellow Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall, MC #3190 Berkeley, CA 94720 510-642-5554 edohare@berkeley.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Douglas N Greve
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Elizabeth O'Hare -
Nathan Dankner