Hi Ziad, Thank you so much for the suggestions. However, I'm not really sure how to utilize any of them...So I guess more detailed help would be necessary for me to follow these suggestions. Sorry.
I've also never actually used SUMA. Previously I was just using a 3dcalc command to bring aseg ROIs into AFNI space. I'm not sure if this will make a difference, but I'm dealing with an averaged subject made with the 'make_average_subject' command (rather than fsaverage). Paul On Tue, 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<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 > > > -- 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
