Hi Ed, the problem appears to be with the initialization. For some reason, fslregister is not initializing this data well. I don't know why the call directly to flirt works (and I've verified here that it does). When I initialize by hand or with SPM, bbregister works fine with the standard arguments. I'll need to dig into the flirt issue more. doug
On 07/17/2012 10:39 AM, Ed Gronenschild wrote: > Hi Doug, > > I've found a solution to the problem: I converted T1.mgz and > FLAIR.mgz to nii.gz and then applied flirt directly with the > same options as in flsregister called by bbregister, > so > > flirt -cost corratio -dof 6 -searchx -90 90 -searchy -90 90 \ > -searchz -90 90 -in FLAIR.nii.gz -ref T1.nii.gz \ > -out FLAIR_to_T1.nii.gz > > This perfectly matched the T1. > > Cheers, > Ed > > On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > >> Message: 18 >> >> Date: Mon, 16 Jul 2012 11:32:06 -0400 >> >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> Subject: Re: [Freesurfer] How to register FLAIR to T1? >> >> To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> >> Message-ID: <500433f6.8010...@nmr.mgh.harvard.edu >> <mailto:500433f6.8010...@nmr.mgh.harvard.edu>> >> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Often with FLAIR there is not enough gray-white contrast to run the >> >> registration. Try using the pial surface instead, with "-surf pial --t1" >> >> This tells it to use the pial surface as a boundary. The --t1 is needed >> >> because the intensity should go from bright to dark. Let me know if that >> >> does not fix the problem. >> >> doug >> >> >> On 07/10/2012 11:58 AM, Bruce Fischl wrote: >> >>> glad to hear it :). You may need to repost (and possibly upload your >>> >>> data) >>> >>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>> >>> >>>> Hi Bruce, >>>> >>>> >>>> It is indeed from the same scan session. >>>> >>>> I'll wait patiently, let Doug enjoy his vacation before >>>> >>>> he gets bothered again by all our questions. >>>> >>>> >>>> Cheers, >>>> >>>> Ed >>>> >>>> >>>> On 10 Jul 2012, at 16:57, Bruce Fischl wrote: >>>> >>>> >>>>> Hi Ed, >>>>> >>>>> >>>>> sorry, you'll have to wait until Doug is back from vacation. Is >>>>> this from >>>>> >>>>> the same session? I've always had it work on flair images using >>>>> one of the >>>>> >>>>> types of initialization. >>>>> >>>>> >>>>> cheers >>>>> >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>>> >>>>> >>>>>> Hi Bruce, >>>>>> >>>>>> >>>>>> Unfortunately, this has no effect. >>>>>> >>>>>> >>>>>> Ed >>>>>> >>>>>> >>>>>> On 10 Jul 2012, at 16:40, Bruce Fischl wrote: >>>>>> >>>>>> >>>>>>> Hi Ed >>>>>>> >>>>>>> >>>>>>> you are using -t2, right? You can also try -init-header >>>>>>> >>>>>>> >>>>>>> cheers >>>>>>> >>>>>>> Bruce >>>>>>> >>>>>>> On Tue, 10 Jul 2012, >>>>>>> >>>>>>> Ed Gronenschild wrote: >>>>>>> >>>>>>> >>>>>>>> Hi Bruce, >>>>>>>> >>>>>>>> >>>>>>>> It is slightly better but still displacements >>>>>>>> >>>>>>>> in all directions and rotations too exist. >>>>>>>> >>>>>>>> >>>>>>>> Ed >>>>>>>> >>>>>>>> >>>>>>>> On 10 Jul 2012, at 16:13, Bruce Fischl wrote: >>>>>>>> >>>>>>>> >>>>>>>>> try -init-spm >>>>>>>>> >>>>>>>>> >>>>>>>>> cheers >>>>>>>>> >>>>>>>>> Bruce >>>>>>>>> >>>>>>>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I would like to register FLAIR to T1. >>>>>>>>>> >>>>>>>>>> Specifications FLAIR: >>>>>>>>>> >>>>>>>>>> axial acquisition, 24 slices, >>>>>>>>>> >>>>>>>>>> pixel size = 0.45 * 0.45 mm^2 >>>>>>>>>> >>>>>>>>>> slice thickness = 5.50 mm (no gap). >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The slices run from the top of the brain >>>>>>>>>> >>>>>>>>>> to just below the eyes. This is contrary >>>>>>>>>> >>>>>>>>>> to the T1 scan which covers the full head >>>>>>>>>> >>>>>>>>>> down to the neck. >>>>>>>>>> >>>>>>>>>> I have tried bbregiser as follows: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> bbregister --s 001 --mov 001_FLAIR.mgz \ >>>>>>>>>> >>>>>>>>>> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> and inspected the result with >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> tkregister2 --mov 001_FLAIR.mgz \ >>>>>>>>>> >>>>>>>>>> --reg 001_register.dat --surf >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The result looks bad, it is displaced and rotated >>>>>>>>>> >>>>>>>>>> by about 20 degrees with respect to T1. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> It makes hardly any difference if instead of --t1 >>>>>>>>>> >>>>>>>>>> --t2 as contrast setting was used. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Is there a better way to do this registration? >>>>>>>>>> >>>>>>>>>> For instance, should I crop T1 to about the >>>>>>>>>> >>>>>>>>>> same space as covered by FLAIR? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> (FreeSurfer v4.5.0, MacOSX 10.5) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Cheers, >>>>>>>>>> >>>>>>>>>> Ed >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> >>>>>>>>>> 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 >>> >>> >>> >> > > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
