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" <[email protected]> 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, [email protected] a écrit : >> Send caret-users mailing list submissions to >> [email protected] >> >> 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 >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> 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 <[email protected]> >> To: "Caret, SureFit, and SuMS software users" >> <[email protected]> >> Subject: Re: [caret-users] Surface-Volume registration >> Message-ID: <cf5af822.c414e%[email protected]> >> 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" <[email protected]> >> 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 >>>[email protected] >>>http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> End of caret-users Digest, Vol 124, Issue 15 >> ******************************************** >_______________________________________________ >caret-users mailing list >[email protected] >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
