I will try that. Have a good day!
Date: Wed, 8 Oct 2014 14:07:38 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs you would have to first run recon-all -all on the T1 On Wed, 8 Oct 2014, Vilde wrote: > Thank you Bruce! > > If I understand you correctly, would the command be > > Recon-all -s subj_name -FLAIRpial.nii ? > > Or would I first have to do recon-all with only T1 as input and then do > another command after it has finished running? And in that case, what would > that command be? > > Best, > Vilde > > Date: Wed, 8 Oct 2014 11:56:51 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs > > Hi Vilde > > no, you can't give recon-all a flair directly, it needs a T1 do do the > recon on. You use the flair at the end to do a post-hoc deformation using > -flairpial I believe > > cheers > Bruce > > > On Wed, 8 Oct 2014, Vilde wrote: > > > Dear mailing list, > > I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for > > pial surface refinement. This results in an error message saying the > > dimensions are mismatched. (The third dimension of the T1 and Flair are > > different by one slice. ) I do not, however, have a problem running > > recon-all with only one T1 input. I am using Freesurfer v 5.1 . > > > > I read in the release notes that in version 5.2 you can use the flag -FLAI > R > > when you are using a flair image as input. I suppose this will not run in > an > > earlier version? > > Would it be correct to use the following command : > > > > recon-all -s [subject] -i T1.nii -i flair.nii -all > > > > Kind regards, > > Vilde > > > > > > > > _______________________________________________ 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.
_______________________________________________ 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.
