Hi,
Neither the registration nor the unwarping seem to failed.
All stages of the registration (example_func -> intiial_highres, initial_highres -> highres, highres -> standard) seem to be worked fine:
http://www.sas.upenn.edu/~mspits/feat_sample/reg/example_func2initial_highres.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/initial_highres2highres.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/highres2standard.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/example_func2highres.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/example_func2standard.png
The field map unwarping also seems to be fine:
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/fieldmap2edges.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/fmap+mag.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/FM_UD_sigloss+mag.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/FM_UD_fmap_mag_brain2str.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/EF_UD_shift+mag.png
http://www.sas.upenn.edu/~mspits/feat_sample/reg/unwarp/initial_highres_distorted2highres.png
Rendered zstat:
http://www.sas.upenn.edu/~mspits/feat_sample/rendered_thresh_zstat1.png
Any ideas?
Thanks,
Manuel
On Apr 2, 2014, at 2:46 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi - have you looked through the "registration" and "unwarping" parts of the HTML output by FEAT, to see which stage of the registrations failed?
> Cheers.
>
>
>
> On 1 Apr 2014, at 23:40, Manuel Spitschan <[log in to unmask]> wrote:
>
>> Hi FSL experts,
>>
>> I'm resurrecting a thread/problem that has come up on the listserv before (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1310&L=fsl&F=&S=&P=23632; in fact, Mark Jenkinson replied but we missed his response) and which hasn't been solved.
>>
>> When I analyze my data with B0 correction and two-step registration ([68mm slab EPIs] --(6df)--> [whole-brain EPI as initial_highres] --(BBR)--> [MPRAGE as main_highres]), I end up with with activation maps in which the overlay of the activation appears to be scaled and placed in the left corner of the image. I'm attaching an image, taken directly from the FEAT report, below.
>>
>> The problem appears to be due to a mis-registration of the statistical maps with example_func, since opening e.g. zstat1.nii.gz as an overlay to example_func in FSLView shows the same problem — see screenshot attached below.
>>
>> When registering directly from slab EPI to the MPRAGE without using the whole-brain as an intermediate, the problem does not occur, but of course the registration is generally not great. The two-step registration could also be performed manually outside of FEAT but I would prefer to stay within the FEAT pipeline.
>>
>> Is this a known and/or common problem, and if not, what could be causing it? Do you have any suggested fixes?
>>
>> I'm happy to upload an example FEAT dir of analysis that shows this problem.
>>
>> FSL version is 5.0.4; no errors appear in the report log.
>>
>> Thanks in advance,
>>
>> Manuel
>>
>>
>> <Screen Shot 2014-02-19 at 5.32.54 PM.png>
>>
>> <rendered_thresh_zstat1.png>
>
>
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> Associate Director, Oxford University FMRIB Centre
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