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.
