From the output it looks like the func-anat registration is off, probably because of the partial FoV is causing the FSL registration used to init BBR to be off (often happens with a partial FoV). Were the anatomical and functional acquired at the same time? If so, then you'll have to bypass reg-feat2anat to create the registration.
Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std doug On 02/02/2014 05:59 PM, Mariam Sood wrote: > Hello Doug, > Thank you for your reply. I tried to investigate it further and would be > grateful for your advice. While the reg-feat2anat registration (default FSL > option) looks way off, the FEAT generated registration, both > functional-anatomical and functional-standard look fine. I have used > brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ > option selected for functional-standard registration and linear 12DOF for > registration to standard). This is a partial FOV image and the determinant of > functional & anatomical have opposite signs. Attached, please find my > reg-feat2anat log file. > > Also from your reply, what I understood is that exf2std.reg.dat is generated > by FSL routines. Won’t exf2anat registration play any part in this? > > I also have a T1-weighted alignment scan acquired with the same orientation > and slice-block centre as the functional data. Is it possible to make use of > this to get better registration should other methods fail? > > Many thanks, > Mariam. > > > > > > On 30 Jan 2014, at 17:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> The second warning you don't need to worry about. I should change that >> to not be a warning. reg-feat2anat is only registering the functional >> and anatomical. If the registration to mni152 does not look good, then >> that is an FSL issue >> doug >> >> On 01/30/2014 11:06 AM, Mariam Sood wrote: >>> Hello, >>> >>> I am running reg-feat2anat and facing some problems. >>> >>> First I ran the command in its default mode using FSL initialisation >>> /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad >>> registration. There is a warning coming up >>> ///WARNING: //initial G-W contrast is negative, but expecting positive./ >>> / If the mov data has a T1 contrast, re-run with --T1/ >>> >>> Next I tried the command using -spm option. The within-subject >>> registration (anat2exf) looks good, but the registration to the >>> standard does not look that good, although not as bad as with -fsl >>> option. >>> >>> The structural and the functional are using different conventions >>> (structural is in radiological convention, whereas functional is >>> neurological). I presume the determinants are associated with this and >>> they have opposite signs. The orientations are also different. >>> Additionally in both the log files (one with -fsl option and -spm >>> option), I get another warning /WARNING:: Flipping Left/Right >>> orientation (as det < 0). /Not sure whether this warning is something >>> I should worry about. >>> >>> Much appreciate your help. >>> >>> Many thanks, >>> Mariam. >>> >>> >>> >>> >>> _______________________________________________ >>> 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: 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 >> >> >> 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 -- 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
