Frank, can you send the commands you used and the terminal output? doug On 01/09/2014 04:35 AM, Frank Hsieh wrote: > 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 <mailto: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 <mailto: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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto: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 <mailto: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
-- 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
