Hi again
Yes, test.nii is the functional data registered to the anatomy.
The following files have now been uploaded to your filedrop and can be
downloaded by the email account "gr...@nmr.mgh.harvard.edu"
1. vol0001.nii.gz : functional input
2. orig.mgz : anatomical target
3. register-test.dat : Output Freesurfer registration file
4. test.nii : Output functional data registered to anatomy
Thank you for helping us,
Erlend
And the functional is test.nii.gz? If so, can you upload
vol0001.nii.gz, register-test.dat, test.nii.gz, and orig.mgz to our file drop?
doug
On 04/25/2012 07:49 AM, Erlend Hodneland wrote:
> Both the fmri data registered to orig is mismatched, and also the original
> raw fmri data are mismatched with orig,
> see the link here showing our raw data (fmri, orig and 152MNI) shown in
> fslview
>
> http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a
>
>
> It is orig.nii converted from orig.mgz that we show yes.
>
> Erlend
>
>
> What images are mismatched? Specifically, which anatomical image are you
> loading into fslview?
> If you have not loaded the orig.mgz (converted to nii), then there will be be
> a
> mismatch.
> doug
>
>
>
> On 04/24/2012 04:29 AM, Erlend Hodneland wrote:
> > 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