Hi Mark,
thanks for your quick response; I've uploaded the cropped + reoriented T1 image I've been using.
The reference code is: 406859.
For clarification: The error occurs only in FEAT registration, not when I'm using FLIRT (in the gui).
And FLIRT didn't create a folder: I did that, and FLIRT popped an image into it. So in FLIRT, I
could register the T1 image to standard space, but in FEAT, that seemed to be the cause of
the problem (because, in FEAT, I could register the 4D data to standard space, but not via the T1
to standard space).
Thanks a lot for your help!!!
Best,
Stefanie
_________________________________________________________________________________
Hi Stefanie,
I'm not sure what exact commands you are running for FLIRT, but it
certainly never creates a directory - only images. From reading your
email it seems like the problem with FEAT is your highres T1 to standard
registration - is that right? In the title of your email you say that epi to T1
doesn't work, but in the email you say that the registration of the 4D data
to the main structural is "not a problem".
What happens when you try to run FEAT with the non-linear registration
turned off? Does that still run for a long time or not?
If you are still having trouble then feel free to upload the structural T1 image
to our upload site at: http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and also send us the reference number.
All the best,
Mark
On 24 Aug 2011, at 11:29, Stefanie Becker wrote:
> 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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