Dear FSL-experts,
I've got a problem registering functional images to the T1-weighted image. In the registration tab in Feat, I'm loading the T1-"betted"-_brain-image as main structural image and the MNI152_T1_2mm_brain-image as standard image. Feat computes all the contrasts etc. but never goes through with the registration; it just keeps hanging. Registration of the 4D-data to the main structural image without the T1 structural image is not a problem (but looks quite rough, as expected).
The standard image and T1 structural image have the same orientation and I have tried 6DOF, 7DOF and 12DOF... all to no avail. The images are from a 3T Siemens scanner, and I used the mricron converter to convert it to FSL format (nii.gz; changing 4D to 3D for the structural). So far I've tried registration with a correctly oriented image, a correctly oriented + cropped image and even with the wrongly oriented image... all with the same result: Registration in FEAT didn't complete and kept "STILL RUNNING" (for hours).
FLIRT registration of the T1 structural to the standard brain seemed to work, although I'm not sure what results to expect from FLIRT -- I specified a new output folder and got a brain. (I also got a brain when I registered the thresholded z-stat-image to my T1-image with FLIRT, which was a bit of a surprise... (?))
I'm using two different FSL versions; an older one with Fedora 9, and the latest version on an FSL_VM with Windows 7; both versions showed exactly the same behaviour, and both versions passed the intial fMRiB-data test.
Any help would be greatly appreciated!!!
Cheers,
Stefanie
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