Matthew,
Thank you for the helpful clarification. I did not realize that. One new question now though...
Upon further inspection, (though the registration performs better without BBR) I tried rolling back to FSL 4.1 and noticed that in the unwarping section under the "Unwarping shift map, in voxels" the images are VERY different between FSL 5 and FSL 4.1... In FSL 4.1 the brain is centered in the field of view, but in FSL 5 it is severely out of place (very posterior in the field of view) so much so that a posterior portion of the brain is outside the field of view. Anybody have any guesses why this might be or suggestions for things to check?
Thank you all for being so patient with my questions.
Warm Regards,
Eric Earl, Research Assistant 2
Fair Neuroimaging Lab
Phone: 503.418.1894 Fax: 503.494.9988
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matthew Webster
Sent: Friday, January 03, 2014 5:32 AM
To: [log in to unmask]
Subject: Re: [FSL] FSL5 FEAT6 epi_reg problems with FLIRT BBR on monkeys
Hello Eric,
It looks like you are using B0 unwarping in your design.fsf? If that is the case then BBR registration _must_ be used.
Kind Regards
Matthew
Hi All,
I did not hear back from Stephen again and I contacted a colleague in another lab doing similar work. My colleague also said he thinks there's a bug in FSL5/FEAT6 where BBR or 6 for the reghighres_dof always goes to BBR anyway. Can someone check into this or tell me which code/script to look at and I'll check into this? Thank you.
Warm Regards,
Eric Earl, Research Assistant 2
Fair Neuroimaging Lab
Phone: 503.418.1894 Fax: 503.494.9988
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Eric Earl
Sent: Friday, December 27, 2013 12:49 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] FW: FSL5 FEAT6 epi_reg problems with FLIRT BBR on monkeys
Stephen,
Thank you so much for the fast response. So, I have tried that before and I tried it again today. When I set the reghighres_dof to 6, it switches itself back to BBR for some unknown reason (both on the command line and in the FEAT6 GUI). Here is the relevant FSF line:
# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) 6
I included the updated FSF file attached as well. Maybe see if it does the same to you?
Warm Regards,
Eric Earl, Research Assistant 2
Fair Neuroimaging Lab
Phone: 503.418.1894 Fax: 503.494.9988
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith
Sent: Friday, December 27, 2013 12:24 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] FW: FSL5 FEAT6 epi_reg problems with FLIRT BBR on monkeys
Hi - so it may be that the stuctural-based tissue segmentation that BBR needs is not working. If plain flirt is working fine, then just select that inside FEAT (eg 6DOF or 7DOF).
Cheers.
On 26 Dec 2013, at 20:42, Eric Earl <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear FSL People,
I am using FEAT6 in FSL5 which is causing serious problems for my EPI (example_func) to T1 (highres) registration for rhesus macaque monkey data. I have attached my FSF file and the registration of EPI to T1 PNG image from the FEAT report. I am using nonlinear registration from highres to atlas (an appropriate monkey atlas) and a diffusion field map.
It looks to me like the problem originates in the epi_reg script, specifically on the FLIRT step that uses BBR for the cost function instead of just using mutual information or possibly correlation ratio. Testing the FLIRT command outside of the epi_reg gives a good registration with a mutual information cost function used in place of the BBR cost function.
Any help or ideas would be appreciated. Thank you all in advance.
Warm Regards,
Eric Earl, Research Assistant 2
Fair Neuroimaging Lab
Phone: 503.418.1894 Fax: 503.494.9988
[log in to unmask]<mailto:[log in to unmask]>
Oregon Health and Science University
Department of Behavioral Neuroscience
3181 SW Sam Jackson Park Road, L470
Portland, OR 97239
http://www.ohsu.edu/fair-lab
<design.fsf><example_func2highres.png>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
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