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 greve@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.
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