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.
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