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