Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site<http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/>to obtain my ROIs. Any thoughts?
Many thanks! Frank On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga < gariko...@gmail.com> wrote: > Hi, > sorry to jump in, but maybe this solves your problem. What I've been doing > is: > > 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert > --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii > > 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select > it in the menu and just save it as *_mricron.nii again. (I converted > nu.mgz with the same procedure as above to check that the roi was in > place). This was the only way to make it visible in fslview and work with > the roi in fsl afterwards. > > > Hope this workaround works for you! > Gari > > > On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> what was your mri_label2vol command and terminal output? >> doug >> >> On 01/06/2014 02:35 AM, Frank Hsieh wrote: >> > Dear FreeSurfer Users, >> > >> > I ran recon -all on my structural image and created ROI masks (using >> > mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like >> > to use these masks for further analysis with FSL. However, it seems >> > that the ROI masks generated with mri_label2vol have different header >> > information than that of the original structural image. As a result, I >> > was unable to carry out further analysis with FSL (e.g., converting >> > these ROI masks into functional space with hires2example_func.mat). I >> > was wondering if there is a way to solve this issue. >> > >> > Many thanks in advance. >> > Frank >> > >> > >> > _______________________________________________ >> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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 >> >> >> 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. >> >> > > _______________________________________________ > 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. > > -- Frank
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