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 "greve@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:
- 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
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