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
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