Hi again, We are trying to do the same as was done in Trachtenberg et al 2012 (Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT registration in FEAT with BBreg:
"For group analysis, functional data were registered, via the high resolution anatomical image, to the Montreal Neurological Institute (MNI) standard brain. Functional data were aligned to the anatomical image initially using FMRIB's Linear Image Registration Tool, (FLIRT) ([Jenkinson and Smith, 2001] <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib27> and [Jenkinson et al., 2002] <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib28>), then optimized using the Boundary-Based Registration (BBR) approach (Greve and Fischl, 2009 <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib21>). Registration from anatomical to standard space was carried out using FMRIB’s Non-Linear Image Registration Tool (FNIRT)." That is, flirt from fmri --> brain, then initializing bbregister fmri --> brain by the previous flirt registration, then flirt and fnirt from brain --> standard space and finally fmri --> standard space and putting all these transformations together. However, our images are orientad as follows from top -> bottom (fmri, orig, 152MNI): http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a As shown in the previous communication, when we directly apply the images to the registration the results are oriented incorrectly, as the input images. Can you recommend a specific solution to overcome the orientation mismatch in these images which is compatible with the registration tasks? Thank you for your patience and help! All best E.H. Hi Erlend, while the images in the tkregister2 pics are oriented correctly the registration is way off. What images are you loading into fslview? You'll need to convert the orig.mgz into nii and load that to check the registration. doug On 04/22/2012 04:16 AM, Erlend Hodneland wrote: > Hi again, > > the registration looks fine in tkregister2, but is apparently wrong in > fslview (and also mricron). See the attached files (as link from > http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing > screenshots of fslview and tkregister2. How can this be explained, and > how can we visualize the correct orientation in fslview? > What does this misalignment influence any further processing with > fnirt and concatenation of the affine transformation fields? > > This is our command we run for bbregister: > > bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat > --init-fsl --t2 --o test.nii.gz > > where vol0001 is the first volume in the fmri sequence and is flipped > to align with LAS (as the highres). > > Thank you for your kind help, > > Erlend Hodneland > > ean that it is in the wrong orientation? It should be in > the same orientation as the anatomical. How does the reg look in > tkregister2? Note that fslview can display volumes in odd orientations > even when the orientation is correct. > doug > > On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > > Hi, > > > > we are trying to register fmri FEAT data (example_func.nii) to the > > anatomical scan (processed in Freesurfer) using bbregister to opt. > > the affine registration before running FNIRT. > > > > However, the orientation of the registered image is flipped around and > > is incorrect after applying bbregister. > > > > We have tried: > > > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat --init-header --bold --o example_func2highres-fs.nii > > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat --init-fsl --bold --o example_func2highres-fs.nii > > 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat > > "myfeatdirectory" > > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > > (this one looks correct) > > followed by > > bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat > > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > > > 5) reorienting to match the highres: > > > > fslorient -swaporient example_func > > fslswapdim example_func x -y z example_func_swap (correct > > orientation) > > > > followed by > > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > > register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii > > > > with the output being flipped in wrong orientation for all options. > > > > We would greatly appreciate if you have any suggestions for how to > > overcome this problem! > > > > Cheers/Sincerly/All best > > > > Erlend Hodneland > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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