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Hi, Mark, Great thanks! You are right!!! Last tonight, I figured it out when I was nearly giving up. I suddenly realized the reason of the problem may be FOV. So, I make the bcot1 and roi the same FOV and voxel size using flirt -usesqform before applying *****. Thanks again! Best, Zhijang Wang 2014-04-08 14:15 GMT+08:00 Mark Jenkinson <[log in to unmask]>: > Hi, > > If I assume that the names bcoT1 (in the initial flirt commands) is > equivalent to nbT1 (in the header info section) and that roi (flirt calls) > is equivalent to ROImask (headers), then I think I see what the problem is. > These images have completely different voxel sizes, and now I suspect that > they also have different FOV. In order to apply one transform to another > image, the second image has to be in the same space as the original input > image. So that means that the voxel size and FOV should be the same for > "bcoT1" and "roi". You should be able to overlay these two images within > FSLView. If not, then you cannot apply the transformation as the image > "roi" is not in the correct space to start with. > > Normally I would expect that "roi" is just a copy of the image "bcoT1" > but the intensities contain zeros everywhere except for within the ROI, > where they would contain the value 1. > > If you describe what "roi" is, and how it relates to "bcoT1" then we > should be able to help. > > All the best, > Mark > > > > On 6 Apr 2014, at 10:09, Zhijiang Wang <[log in to unmask]> wrote: > > 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, >> >> >> > >