Completely removing sform and qform will result in a volume with coordinates (0, 0, 0) at a corner of the FOV, this is almost certainly not what you want. What you probably want is the sform and qform to both be valid, and to match, and the matrix to have zeros except on the diagonal and last column (and last row is always 0 0 0 1), something like this:
... qto_xyz:1 -1.000000 0.000000 0.000000 84.904289 qto_xyz:2 0.000000 1.000000 0.000000 -55.609478 qto_xyz:3 0.000000 0.000000 1.000000 -135.906647 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 ... and the same exact values for the sform matrix I don't think the exact values of the last column matter much at this point, since I don't think you've done volume registration yet. Tim On Fri, Mar 28, 2014 at 3:09 PM, Matt Glasser <m...@ma-tea.com> wrote: > All that matters is that they are not oblique. If they are oblique > FreeSurfer, FSL, and Caret will not work well together. I don¹t know that > setting the code is sufficient. > > Peace, > > Matt. > > On 3/28/14, 2:44 PM, "Righart, Ruthger" <righ...@lrz.tu-muenchen.de> > wrote: > > >Dear Matt > >I removed the sform from the t1.nii, before mri_convert makes it > >001.mgz, so at the start of Freesurfer (sform_code='0'). > >But do I understand correctly from your mail that both sform and qform > >should be removed? (i.e., sform_code='0' and qform_code='0' in the > >header). If so then that might be the reason. > >Best, > >Ruthger > > > >Le 2014-03-28 18:00, caret-users-requ...@brainvis.wustl.edu a écrit : > >> Send caret-users mailing list submissions to > >> caret-users@brainvis.wustl.edu > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> or, via email, send a message with subject or body 'help' to > >> caret-users-requ...@brainvis.wustl.edu > >> > >> You can reach the person managing the list at > >> caret-users-ow...@brainvis.wustl.edu > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of caret-users digest..." > >> > >> > >> Today's Topics: > >> > >> 1. Re: Surface-Volume registration (Matt Glasser) > >> > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 28 Mar 2014 09:58:32 -0500 > >> From: Matt Glasser <m...@ma-tea.com> > >> To: "Caret, SureFit, and SuMS software users" > >> <caret-users@brainvis.wustl.edu> > >> Subject: Re: [caret-users] Surface-Volume registration > >> Message-ID: <cf5af822.c414e%m...@ma-tea.com> > >> Content-Type: text/plain; charset="US-ASCII" > >> > >> Did you remove the sform and qform at the beginning of the process > >> (i.e. > >> before FreeSurfer)? > >> > >> Peace, > >> > >> Matt. > >> > >> On 3/28/14, 9:04 AM, "Righart, Ruthger" <righ...@lrz.tu-muenchen.de> > >> wrote: > >> > >>>Dear Caret experts, > >>> > >>>I am working on myelin mapping but encounter errors in surface-volume > >>>registration, as previously reported in this list. > >>> > >>>I have removed oblique sforms from the t1.nii and t2.nii files > >>>(sform_code='0' and qform='1', the new headers have equal matrices > >>> for s > >>>and q). > >>>I have the impression that the first error occurs after the command: > >>> > >>>applywarp --interp=spline -i OrigT2w.nii.gz -r T1w.nii.gz > >>>--premat=T2w2T1wbb.mat -o T2w2T1w_translated.nii.gz > >>> > >>>Please find attached an fslview for the translated and non-translated > >>>images. The translated image is not centered and from the > >>> non-translated > >>>images a piece of the left hemisphere is cut-off (I wondered if this > >>> has > >>>anything to do with the coordinate space, Scanner Anat(1) or Aligned > >>>Anat(2) in the headers?). I would welcome your suggestions to solve > >>> this > >>>problem. I am working with Caret v5.65 on a Linux machine. Thank you > >>>very much in advance! > >>> > >>>Ruthger_______________________________________________ > >>>caret-users mailing list > >>>caret-users@brainvis.wustl.edu > >>>http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> End of caret-users Digest, Vol 124, Issue 15 > >> ******************************************** > >_______________________________________________ > >caret-users mailing list > >caret-users@brainvis.wustl.edu > >http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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