Thanks Ziad Bruce
On Feb 19, 2013, at 10:42 PM, ziad <ziad...@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 <fis...@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 >> -- >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> -- >> 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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