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%abstract the fourth, fifth and sixth volume from the txt file obtained in the last step.
Y1=Y(:,4);
Y2=Y(:,5);
Y3=Y(:,6);
% Then calculate
for a=1:1:63
RX=[cos(Y1(a)) sin(Y1(a)) 0;
-sin(Y1(a)) cos(Y1(a)) 0;
0 0 1];
RY=[cos(Y2(a)) sin(Y2(a)) 0;
-sin(Y2(a)) cos(Y2(a)) 0;
0 0 1];
RZ=[cos(Y3(a)) sin(Y3(a)) 0;
-sin(Y3(a)) cos(Y3(a)) 0;
0 0 1];
x'(a)=(inv(RX*RY*RZ))*X
end
Dear Lulu,
I checked the qform/storm in these three b0 images, and found that qform of b0_19.nii.gz image scanned by the 19 orientation gradient table was different from the other two. I listed them below. Is there any way for me to solve this problem?(1) b0_19 orientations:
qto_xyz:1 -1.718750 0.000000 -0.000000 109.325317 qto_xyz:2 0.000000 1.691586 -0.301044 -80.299522 qto_xyz:3 0.000000 0.304364 1.673132 -40.676346 qto_xyz:4 0.000000 0.000000 0.000000 1.000000
(2) b0_20/21 orientations:
qto_xyz:1 -1.718750 0.000000 -0.000000 107.975891 qto_xyz:2 0.000000 1.691586 -0.301044 -81.648949 qto_xyz:3 0.000000 0.304364 1.673132 -40.676346 qto_xyz:4 0.000000 0.000000 0.000000 1.000000
It looks like there was some small repositioning of the subject between the two runs. For the future, try to avoid that if possible. For now I don't think that is a problem. I think the message from fslmerge would just have been a warning to let you know what had happened, but that it still merged the files. It should be easy for you to check using fslview. It means there will be a change in position in the data, but hopefully eddy will be able to detect and correct that.
But, it is still not clear to me if you have acquired data with different blip directions? As I said, your acqparams.txt assumes you have, and it is also the only way in which you will be able to correct for susceptibility distortions.
Jesper
2013/10/7 Jesper Andersson <[log in to unmask]>
Dear Lulu,
I was trying to do pre-processing with our high angular resolution diffusion data from Siemens 3T.The acquisition was divided into 3 consecutive scans of 5 minutes each, to improve the comfort of the subject. They consisted of three blocks of 19, 20 and 21 orientations each. Each of these three acquisitions have one b0 images.I read the manual of fsl's tool 'eddy' and 'topup', and I think that our data could be correctd(eddy current and suscepbility problem) by these two tools (Am I right?).I extracted three b0 images, and tring to merge them together, but it gave me an error:
'fslMerge fault:Inconsistent orientations for individual images when attempting to merge.Merge will use voxel-based orientation which is probably incorrect -*PLEASE CHECK*!'
I am not sure that if this problem is related to my gradient orientation, and if this problem would influence my following processing.
I don't think this has to do with your gradient directions. It sounds either like a round off error in the voxel size fields, or the storm/qform is different. I suggest you use fslhd to check those things.There is documentation about how to write these here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq and here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/Faq.
Another problem is about the acqparams.txt file. Since we have three b0 images, and our phase encoding direction is R>>L, EPI factor is 128, echo spacing is 0.85 ms, I wrote the acqparams.txt file like this" 1 0 0 0.108
-1 0 0 0.108
1 0 0 0.108
-1 0 0 0.108
1 0 0 0.108
-1 0 0 0.108"Is this the right way to write the acqparams file for our three b0 images?
However, it is not clear from your description if you acquired b=0 scans with reversed phase encode blips. Your acqparams file implies you have six b=0 files acquired R->L, L->R, R->L, L->R, R->L, L->R in that order. Is that correct?
JesperThanks in advance!Lulu