Hi Paul, do you still have a problem that needs to be solved? doug
On 02/18/2013 04:39 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 <mailto: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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
