Dear Mark,
Great thanks to your reply!
Please let me re-tell you my question:
#######################################################################
flirt -in bcoT1 -ref B0 -cost corration -o t12b0
-omat t_mat
# t12b0 is OK.
flirt -in roi -ref B0 -o b0_roi -init t_mat
-applyxfm
# But, when applying the transformation matrix to the roi
mask, the resulted b0_roi.nii can not be alighned with b0/
Why?
I am so confused/
############################################################################
I just send my .nii file to you and fsl-email-list, but received "Fail in
sending this email because the size of files is greater than 200K".
So, I have to attach some head information (*.mat, sform, qform).
Could anybody tell me where the problem is?
Great thanks!
B0.head.mat
-2.20312500000000 0 0 143.203125000000
0 2.20312500000000 0 -124.132568359375
0 0 2.20000004768372 -53.7819283008575
0 0 0 1
fslorient -getqform B0
-2.20312 0 -0 141
0 2.20312 -0 -121.929
0 0 2.2 -51.5819
0 0 0 1
fslorient -getsform B0
-2.20312 0 0 141
0 2.20312 0 -121.929
0 0 2.2 -51.5819
0 0 0 1
bT1.head.mat
1.32840895652771 0.0126800928264856 0.0472275912761688 -104.481479177251
-0.0154902637004852 0.999688148498535 -0.0220899917185307 -113.658335920423
-0.0631656423211098 0.0215135142207146 0.998639881610870 -120.418306723237
0 0 0 1
fslorient -getsform nbT1
1.32841 0.0126801 0.0472276 -103.093
-0.0154903 0.999688 -0.02209 -112.696
-0.0631656 0.0215135 0.99864 -119.461
0 0 0 1
fslorient -getqform nbT1
1.32873 0 0.0436194 -99.8026
0 1 0 -80.1566
-0.0580138 0 0.999048 -101.699
0 0 0 1
ROImaskfile.head.mat
-3.12486195564270 -0.0109078036621213 0.0366514474153519 101.246426661499
-0.0109082190319896 3.12498092651367 1.35525271560688e-20 -122.445417311974
0.0272702574729919 9.51912588789128e-05 4.19984006881714 -71.5327780273146
0 0 0 1
fslorient -getsform ROImask
-3.12486 -0.0109078 0.0366514 98.1473
-0.0109082 3.12498 1.35525e-20 -119.331
0.0272703 9.51913e-05 4.19984 -67.3056
0 0 0 1
fslorient -getqform ROImask
-3.12486 -0.0109078 0.0366216 98.1473
-0.0109082 3.12498 -5.22123e-08 -119.331
0.0272481 9.51524e-05 4.19984 -67.3056
0 0 0 1
2014-03-10 19:08 GMT+08:00 Mark Jenkinson <[log in to unmask]>:
> Hi,
>
> It is difficult to know what is going wrong from your description here.
> The commands, subject to minor typos (e.g. corration), look correct.
> Could the problem be related to the output of the second command not using
> a floating-point datatype (you can fix this with "-datatype float" in the
> second flirt call) and hence it truncating a lot of the mask values to zero?
>
> If that is not the case then please give us a more informative
> description of the problem.
>
> All the best,
> Mark
>
>
>
> On 4 Mar 2014, at 13:15, Zhijiang Wang <[log in to unmask]> wrote:
>
> Dear fslers,
>
> I want to register a ROI mask into B0, but I am confused the followings:
>
> flirt -in bcoT1 -ref B0 -cost corration -o t12b0 -omat
> t_mat
>
> # t12b0 is OK.
>
> flirt -in roi -ref B0 -o b0_roi -init t_mat -applyxfm
> # But, when applying the transformation matrix to the roi mask, the
> resulted b0_roi.nii can not be alighned with b0/
>
> Why?
>
> I am so confused/
>
> who can share with your suggestions and comments.
>
> Best,
>
>
>
