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>Understood. Thanks for your explaination. I noticed that with registerering MTR deskulled brains to T1, I can only do so with flirt with 12dof affine and not 6 or 9 dof. May I ask why does 6DOF works for undistorted fa but not for MTR images? Thanks Siewmin I'm sorry, I think I misunderstood you somewhere along the way and that is > the source of our confusion. You are correct that the 1mm and 2mm > templates > have different matrix sizes (this is what I didn't realize you were > referring to). I thought you had some other version of the MNI template > that had more empty space around it (a bigger FOV). The FOV actually is > exactly the same, it is just the matrix that is larger in the 1mm (as it > divides the same FOV into smaller voxels). There will be no translational > difference in the images (I just verified this by resampling the 2mm > template to the 1mm template using an identity matrix). If your images > had > different FOVs, rather than different matrix sizes, you cannot necessarily > just resample the images with an identity matrix. > > If you look carefully in that config file, you will see that the last > subsampling step is 2 rather than 1 (and hence the highest resolution > reference image used is 2mm). Since you want your transform to be from > the > 1mm MNI space to the 1mm T1 space (and then the FA), you could just edit > the > config file to use the 1mm nonlinearly generated template and double the > numbers in the --subsamp option (i.e. --subsamp=4,4,2,2,1,1 becomes > --subsamp=8,8,4,4,2,2). This will give you what you want without taking > an > inordinate amount of time. > > Hope this clarifies everything. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Siew-Min Gan > Sent: Tuesday, May 19, 2009 4:50 PM > To: [log in to unmask] > Subject: Re: [FSL] choice of registration and MNI template > >>Hi Matt, > sorry I'm a bit unclear now. Do you mean there might be > translational difference in my normalised FA if I use a > 2mm or 1mm MNI template ( with different FOV) for > registration? Is that due to the interpolation when the > normalised FA is resampled? If I'm doing the registration > FA2T1 and T12MNI, so I can get the inverse matrix to > transfer the template rois back to my FA native space, > would this translation still occur when the binary rois > are interpolated via nearest neighbour (i.e the rois > positioning would differ by translation when placed in > the native FA space depending on which MNI template I > use)? > > The fMRIB config file FA_2_FMRIB58_1mm.cnf uses the 1mm. Please correct me > if I'm wrong. > > thanks > > Siewmin > > On the first point, I think you do, but am not 100% sure. The differences >> would only be translational. For the nonlinear registration, the warp >> fields are on the order of 8-10mm in resolution so it never makes a >> difference in the warpfield to register at a higher resolution. What it >> does make a difference in is processing time and resource usage. Thus, >> in >> none of the fMRIB generated config files is a reference image used with >> less >> than a 2mm resolution (or a subsampling step that makes the image 2mm >> internally). >> >> Peace, >> >> Matt. >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf >> Of Siew-Min Gan >> Sent: Tuesday, May 19, 2009 3:15 PM >> To: [log in to unmask] >> Subject: Re: [FSL] choice of registration and MNI template >> >>>Thanks for your reply. >> Can I clarify with you two points? You mentioned I need to take into >> account the FOVs in the applywarp step, do you just mean that my >> transformed FA in MNI space will take on the FOV of the MNI template >> that >> I'm registerering to? >> Secondly, my FA image is 2mm isotropic, my T1 image is 1mm isotropic. >> For >> nonlinear registration of my T1 image to the MNI template, do you mean >> it >> makes no difference for the quality of registration whether I choose the >> 1mm or the 2mm template MNI template? I.e it doesn't make better >> registration if the target image (MNI brain) is same resolution as >> source >> image (my T1)? >> >> Thanks >> >> Siewmin >> >> It really is fine to do the registration in two steps. You just don't >>> want >>> to resample your data (i.e. your ROIs) multiple times, so you can use >>> the >>> options of applywarp to do your resampling in a single step. If, for >>> some >>> reason, you wanted to do quantitative analysis on the FA in MNI space, >>> it >>> would be better register the FA to the T1 and the T1 to the MNI and >>> then >>> use >>> apply warp to move the FA to MNI space in one step. Does this make >>> sense? >>> >>> I am not sure what the best way to deal with the different FOVs. One >>> could >>> simply "register" the two templates together using 3 DOF (translations >>> only), however maybe there is a more elegant way... (although voxel >>> coordinates are different, mm coordinates will be the same in both >>> templates). The FOVs will not make a difference for the quality of the >>> registrations, but you might need to take them into account for the >>> applywarp step. >>> >>> Peace, >>> >>> Matt. >>> >>> -----Original Message----- >>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >>> Behalf >>> Of Siew-Min Gan >>> Sent: Monday, May 18, 2009 10:35 AM >>> To: [log in to unmask] >>> Subject: Re: [FSL] choice of registration and MNI template >>> >>>>Thanks. >>> >>> Sory I wasn't clear with the 3rd Question. The two ways mentioned have >>> the >>> similiarity of first registering FA to T1 (linearly) for the same >>> subject. >>> The difference is with the 1st way: >>> after the linear registration of FA2T1, I then nonlinearly register T1 >>> from it's T1 native space directly to MNI standard space. Hence Fa >>> image >>> is moved twice to get into the standard space (Fa2T1 and T12MNI). >>> Likewise >>> the atlas rois from standard space is transformed back to the native FA >>> image via two inverse matrices ( of FA2T1 and T12MNI) >>> With the second way >>> 2) after getting the linear regisration matrix of FA2T1, I apply the >>> inverse of the registration matrix of FA2T1 on the T1 image, moving T1 >>> onto FA image space. I then nonlinearly register this registered T1 >>> (which is now in FA space) onto MNI standard space. This is different >>> to >>> above where the T1 was registered from it's native space. Hence, in >>> contrast to above, the Fa image would only need to move once to get >>> into >>> the standard space via the nonlinear transformation matrix of the >>> registeredT1to MNI.Likewise the atlas rois from the standard space is >>> transformed back to the native FA image via only one inverse matrix ( >>> of >>> the RegisteredT12MNI. >>> >>> I wonder which one would be more accurate to transform the roi back to >>> the >>> native FA space ? >>> >>> With the choice of the MNI template, the ROIs of the atlas are created >>> and >>> drawn on an average dti map which is normalised to the space of the >>> linearly created MNI152 182x218x182 1mm atlas. The MNI152 2mm atlas >>> used >>> in the provided cnf file is nonlinearly created and is of dimension i.e >>> 91 >>> x 109 x91 . If the dimensions and resolution are not important to get >>> the >>> registration matrix to backtransform the standard space rois to native >>> fa >>> image, but would there be some dissimiliarity between the linearly >>> created >>> and the nonlinearly created MNI152 template? Hence, I thought it would >>> be >>> more "accurate" to register to the linearly created MNI template which >>> is >>> used when creating the rois, although this would be at the expense of >>> the >>> registration? Please correct me if I'm wrong. >>> >>> Thanks >>> >>> Siewmin >>> >>> >>> >>> You should use the default file in the T1_2_MNI152_2mm.cnf as that will >>>> give >>>> the best results. That config file is properly tuned to give optimal >>>> T1 >>>> to >>>> MNI template registrations. Why use a worse quality reference image >>>> (the >>>> linear template) with higher resolution (much longer processing time >>>> and >>>> higher resource usage for no benefit in registration quality)? >>>> >>>> Your commands look correct to me. >>>> >>>> 1. Yes >>>> >>>> 2. See above you shouldn't modify the config file. >>>> >>>> 3. I am having some difficulty following you. So long as you have >>>> transformations describing FA -> T1 and T1 -> MNI, you can move >>>> anything >>>> you >>>> want from FA to MNI or MNI to FA. Applywarp will only resample the >>>> images >>>> once, even if you include both a linear and nonlinear transformation >>>> (in >>>> fact you can include up to two linear transformations, one before and >>>> one >>>> after the nonlinear one) so long as you give everything in one >>>> commandline. >>>> You can also combine linear and nonlinear transformations with >>>> convertwarp. >>>> >>>> >>>> 4. Again I don't think you should be using the linearly derived >>>> templates. >>>> >>>> I'm not sure of the best answer to your last two questions. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> -----Original Message----- >>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >>>> Behalf >>>> Of Siewmin Gan >>>> Sent: Monday, May 18, 2009 8:00 AM >>>> To: [log in to unmask] >>>> Subject: [FSL] choice of registration and MNI template >>>> >>>> Hi, I have a few questions about trying fnirt to register fa and other >>>> scalar maps to the >>>> MNI template, so I can use the invert transformations to put the rois >>>> of >>>> the >>>> white matter >>>> atlas back onto the native fa and scalar maps. Apologies for the long >>>> questions. >>>> >>>> I performed linear 6DOF registration of subjects FA to their T1, and >>>> linear >>>> followed by >>>> non_linear registration of T1 to MNI152. The fa and scalar maps are >>>> calculated from 4D >>>> DWI with B0 unwarping/undistortion performed. These maps are 2mm >>>> isotropic >>>> and the >>>> T1 images of the subjects are 1mm isotropic. The MNI template chosen >>>> is >>>> the >>>> MNI_linear >>>> template 1mm. I did this following similiar steps to the 2nd fnirt >>>> example >>>> script on the >>>> fnirt website (i.e fmri to MNI via T1) and with slight modification of >>>> the >>>> T1_2_MNI152_2mm.cnf. May I ask if the following commands are the right >>>> way >>>> and >>>> quickest way to "concantenate" the two inverse linear T12FA matrix and >>>> nonlinear MNI2T1 >>>> warp coefficient to transform binary rois from MNI to the native FA >>>> space? >>>> I have also >>>> listed my questions below about the choice of registration, template >>>> and >>>> using these >>>> appropriate parameters in the config file: >>>> >>>> T1_brain and Image_FA_brain (betted) The Image_FA I have is betted so >>>> I >>>> don't have a FA >>>> image with skull. >>>> >>>> flirt -ref T1_brain -in Image_FA_brain -out FA2T1_brain -omat >>>> FA2T1.mat; >>>> flirt -ref MNI152lin_T1_1mm_brain -in T1_brain -omat >>>> my_affine_transf.mat; >>>> fnirt --in=T1 --aff=my_affine_transf.mat --cout=my_nonlinear_transf -- >>>> config=T1_2_MNI152lin_1mm.cnf; >>>> applywarp --ref=MNI152lin_T1_1mm --in=Image_FA_brain >>>> --warp=my_nonlinear_transf - >>>> -premat=FA2T1.mat --out=my_warped_fa2mni_1mm >>>> >>>> (applying inverse matrix to place ROI from MNI to FA native space) >>>> convert_xfm -omat T12FA.mat -inverse FA2T1.mat >>>> invwarp --ref=T1.nii.gz --warp=my_nonlinear_transf.nii.gz >>>> --out=nonlinear_MNI2T1 >>>> applywarp --ref=Image_FA_brain --in=ROIs_in_MNI_space >>>> --warp=nonlinear_MNI2T1 -- >>>> postmat=T12FA.mat out=ROIs_in_FAnative_space --interp=nn >>>> >>>> >>>> 1. Is it ok that I use a betted FA image all the way in these steps, >>>> as >>>> long >>>> as the T1 >>>> image used in FNIRT is the original T1 with skull on? >>>> >>>> 2. I use the MNI152_lin_1mm template with slight modifications to >>>> T1_2_MNI152_2mm.cnf ( renaming it T1_2_MNI142lin_1mm.cnf ). The >>>> MNItemplate >>>> now >>>> chosen is a lot smoother, is 1mm and of different intensity to the >>>> other >>>> MNI >>>> template >>>> used in T1_2_MNI152_2mm.cnf). Apart from modifying the cnf file by >>>> changing >>>> the MNI >>>> template to the linear 1mm template, and the corresponding brain mask >>>> , >>>> which other >>>> parameters would be important to change (my T1 and the MNIlin_1mm are >>>> both >>>> 1mm in >>>> resolution? Would there be any recommendations you suggest for the >>>> some >>>> of >>>> parameters in the config file in this circumstance: The current >>>> settings >>>> in >>>> the >>>> T1_2_MNI152_2mm config files are >>>> >>>> subsamp:4,4,2,2,1,1 >>>> infwhm: 8,6,5,4.5,3,2 >>>> refwhm:8,6,5,4,2,0 >>>> lambda:300,150,100,50,40,30 >>>> intorder:5 >>>> biasres: 50 50 50 >>>> >>>> 3. If I perform registration of image fa -->t1 -->to mni, without >>>> including >>>> the -out in the >>>> command line, the fa imagehas to be resampled once when nonlinear >>>> transformation to >>>> the MNI 1mm space is performed. Alternatively, I can use the inverse >>>> matrix >>>> of >>>> FA2T1.mat (i.e T12FA.mat) on T1. This will register T1 to FA followed >>>> by >>>> nonlinear >>>> transformation of this registeredT1 to the MNI template to get the >>>> my_nonlinear_transf >>>> matrix file of the T1(inFA native space) to MNI, which I can use to >>>> transform FA to MNI in >>>> one step. With the 1st method, the rois of the white matter template >>>> would >>>> be >>>> transformed onto the raw FA image using the inverse of >>>> my_nonlinear_transf >>>> matrix and >>>> FA2T1.mat as written in the command line above. With the second >>>> method, >>>> only >>>> the >>>> inverse of my_nonlinear_transf matrix would be used, without requiring >>>> the >>>> postmat >>>> T12FA.mat. With the Fa_image contrast and resolution, which way would >>>> be >>>> more >>>> precise/accurate to i) register or normalise ( register and resample >>>> FA >>>> images to MNI >>>> template) and ii) back-register the rois (by neighbouring >>>> interpolation)from >>>> the template >>>> to the raw space of the FA image? >>>> >>>> 4. The rois of the white matter atlas is created when normalising to >>>> the >>>> MNI152_lin_1mm >>>> template and not the MNI152 _1mm (the non linear template which has a >>>> higher >>>> >>>> resolution). If I want to invert transform the rois of the atlas in >>>> MNI >>>> space to the native >>>> space of the fa images, would it be right to use the MNI152_lin_1mm >>>> template >>>> to get the >>>> transformation matrices(because of how the rois of the atlas has been >>>> created), even >>>> though it is of poorer resolution than the other nonlinear MNI >>>> template >>>> ? >>>> >>>> >>>> 5. Is there any output from running the flirt and fnirt that can be >>>> used >>>> to >>>> get a measure >>>> of the precision in the registration methods (apart from visual >>>> inspections), or there a >>>> paper of fnirt that mentioned the precision of fnirt? I read that one >>>> way >>>> to >>>> quantitate the >>>> registration quality of the rois apart from visual inspection is >>>> assess >>>> the >>>> amount of >>>> displacement of x,y, z coordinated of defined landmarks from the MNI >>>> space >>>> when they >>>> are transferred to the normalised FA images? >>>> >>>> 6. Lastly, on the fnirt website, it mentioned that fnirt method is not >>>> diffeomorphic by >>>> consruction with some explainations of the difference. Would that >>>> matter >>>> in >>>> my case >>>> whether I use a diffeomorphic by construction method or not for the >>>> purpose >>>> I'm trying to >>>> achieve here(i.e to try as best to register binary rois from the atlas >>>> to >>>> the native fa >>>> space)? >>>> >>>> Many thanks for your kind patience. >>>> >>>> Siewmin >>>> >>> >> >