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
>