>thanks very much. I reset the pixdim and it worked. with the command
lines for fslmaths. It works too with the command line fslmaths if I
include -max 0 and -odt float.
Siewmin
Hi,
>
> OK, I think this lets me figure a couple of things out.
> Firstly, the fslmaths lines probably need "-odt float" added to the
> end as it sounds like you are working with integer images and
> currently it is rounding the answers to integers at the end which
> is not what you want. The "-odt float" will give you a floating point
> output instead.
>
> As for the avscale results, they show a *huge* scaling - a factor of 2.
> This suggests to me that the images you are matching do not have
> the voxel dimensions set correctly. If you are making one of them in
> matlab then it is likely that this is getting default voxel sizes set
> to 1mm
> when this is not actually true. The voxel size is massively important
> information for registration and if it is not set correctly then
> things just
> will not work.
>
> So check the voxel sizes. The tool fslsize shows you the voxel sizes
> and fslchpixdim allows you to reset them. I would also check on the
> data orientations with fslorient, as they should be the same. If they
> are not then you need to fix this too (with either fslorient or
> fslswapdim).
>
> Hopefully these suggestions will solve your problems.
> All the best,
> Mark
>
>
>
> On 21 May 2009, at 14:11, Siew-Min Gan wrote:
>
>>> Thanks. I've attached the 12dof output matrix run on avscale below.
>>> With
>> the commands you gave me, I tried these fslmaths commands before.
>> For the
>> first command, I get a white box in fslview ( nobrain). With the
>> second
>> command, I get a binary image with the brain as 0 and the nonbrain
>> tissue
>> as 1. I'm not sure why, hence i did the calculations with matlab.
>> Thanks
>> again.
>>
>> Rotation & Translation Matrix:
>> 0.999976 0.005551 -0.004088 -7.866150
>> -0.006757 0.907013 -0.421049 13.451900
>> 0.001371 0.421067 0.907028 -18.613500
>> 0.000000 0.000000 0.000000 1.000000
>>
>> Scales (x,y,z) = 1.915426 1.947678 1.910669
>>
>> Skews (xy,xz,yz) = 0.001418 0.003214 0.027073
>>
>> Average scaling = 1.92459
>>
>> Determinant = 7.128
>> Left-Right orientation: preserved
>>
>> Forward half transform =
>> 1.383981 0.005175 -0.000129 -3.308535
>> -0.004572 1.362760 -0.279752 4.693886
>> 0.001458 0.300895 1.353795 -8.490392
>> 0.000000 0.000000 0.000000 1.000000
>>
>> Backward half transform =
>> 0.722547 -0.002377 -0.000530 2.397223
>> 0.002173 0.704262 0.144634 -2.070535
>> -0.001260 -0.156453 0.703926 6.706810
>> 0.000000 0.000000 0.000000 1.000000
>>
>>
>>
>> Hi,
>>>
>>> I suspect that the problem is these more extreme values
>>> around the brain edge. Are you expecting any true values
>>> to be less than 0? If not, then it would help to remove the
>>> negative values. You can repeat the same calculation in
>>> fslmaths with:
>>> fslmaths mtoff -sub mton -div mtoff mtr_image
>>> or include a lower cutoff at zero as well with:
>>> fslmaths mtoff -sub mton -div mtoff -max 0 mtr_image
>>>
>>> Try this and see if you can get a 6 DOF registration to
>>> work with this image.
>>>
>>> As for the avscale - you seem to have run it on a 6 DOF output.
>>> Can you please run it on the 12 DOF output matrix (in the
>>> same way that you did - no other options are required) and
>>> send me the output then.
>>>
>>> All the best,
>>> Mark
>>>
>>> On 21 May 2009, at 11:52, Siew-Min Gan wrote:
>>>
>>>>> Thanks. There's scaling and skewing of the MTR image registered to
>>>>> the
>>>> same subjects T1 (both deskulled). There is some negative value
>>>> intensities around the edge of the brain of the MTR image. When I
>>>> try
>>>> fslstats MTR_brain.nii.gz -R, I get -72.000000 1.000000. The
>>>> Magnetisation Transfer Imaging Ratio image is derived from [(mtoff
>>>> image-mton images)/mt_off image] in with MATLAB. Is there a fsl
>>>> command
>>>> that can perform this function that I can check if I've done the
>>>> maths
>>>> correctly, although I'm pretty sure the images are subtracted and
>>>> divided
>>>> correctly. I can't get a perfectly deskulled MTR image with BET
>>>> without
>>>> losing some of the brain itself, and the best MTR image betted would
>>>> still have 1-2 pixels of nonbrain around it.
>>>>
>>>>
>>>> When I type avscale, I get
>>>> avscale [--allparams/--inverteddies] matrixfile [non-reference-
>>>> volume].
>>>> What does [--allparams/--inverteddies] mean, and is the
>>>> [non-reference-volume] my betted MTR image?
>>>>
>>>> i typed avscale MTR2T1.mat and this is my output below. Please
>>>> let me
>>>> know if this is not what you need. thanks
>>>>
>>>> Siewmin
>>>>
>>>> Rotation & Translation Matrix:
>>>> 0.995794 -0.021164 -0.089148 7.369500
>>>> 0.060188 0.884693 0.462272 16.040700
>>>> 0.069085 -0.465693 0.882246 76.415500
>>>> 0.000000 0.000000 0.000000 1.000000
>>>>
>>>> Scales (x,y,z) = 1.000000 1.000000 1.000000
>>>>
>>>> Skews (xy,xz,yz) = 0.000000 -0.000000 0.000000
>>>>
>>>> Average scaling = 1
>>>>
>>>> Determinant = 1
>>>> Left-Right orientation: preserved
>>>>
>>>> Forward half transform =
>>>> 0.998933 -0.016017 -0.043333 4.561216
>>>> 0.025922 0.970733 0.238760 3.341746
>>>> 0.038240 -0.239628 0.970111 39.105334
>>>> 0.000000 0.000000 0.000000 1.000000
>>>>
>>>> Backward half transform =
>>>> 0.998932 0.025922 0.038240 -6.138365
>>>> -0.016017 0.970733 -0.239628 6.199851
>>>> -0.043333 0.238760 0.970112 -38.536765
>>>> 0.000000 0.000000 0.000000 1.000000
>>>>
>>>> Hi,
>>>>>
>>>>> I assume MTR is Magnetisation Transfer Ratio - but this doesn't
>>>>> explain why 12 dof works while 6 dof fails. I assume they are of
>>>>> the same subject - right?
>>>>>
>>>>> Is there anything unusual with the intensities around the edge of
>>>>> the brain? And does the 12 dof result do a lot of scaling or
>>>>> skewing?
>>>>> Can you run avscale on the transformation matrix from FLIRT and
>>>>> send us the output?
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>> On 20 May 2009, at 22:12, Matt Glasser wrote:
>>>>>
>>>>>> What is MTR, I don't think I know that acronym.
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>>>>> On
>>>>>> Behalf
>>>>>> Of Siew-Min Gan
>>>>>> Sent: Wednesday, May 20, 2009 6:43 AM
>>>>>> To: [log in to unmask]
>>>>>> Subject: Re: [FSL] choice of registration and MNI template
>>>>>>
>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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