Dear Jesper,
Since our data was scanned in three acquistion, and each has a b0 image
(obtained by Siemens, dcm format), when I tried to merge all dcm files into
a 4D.nii.gz file using mricron, I found that the software
would change all dcm files into three 4D.nii.gz file. So I used the flag
fslmerge to merge them into one 4D file. I wonder that if this was ok, or
there are some other ways to change the dcm files into one 4D file in case
of losing information?
I finished doing eddy using method above, and obtained the
eddy_corrected_data file and the txt file, but I encoutered some problems
about how to rotate the bvecs file. I read the manual here
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/Faq, but I still
couldn't understand how to do rotate the file with my limited knowledge of
scripting. We wrote script below and found that the dimension of X is 3 *
n_volumes, while the dimension of "inv(RX*RY*RZ))"is 3*3. Since formula has
been pre-multiplication, I found it may not be able to multiple them(maybe
I misunderstood this). Would you please give me some suggestions about
this?
%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
If I finished using eddy, do I also need to run applytopup?
Thanks in advance!
Yours,
Lulu
2013/10/10 Jesper Andersson <[log in to unmask]>
> 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.
>>
>> 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?
>>
>>
>> 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.
>>
>> 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?
>>
>> Jesper
>>
>>
>> Thanks in advance!
>>
>> Lulu
>>
>>
>>
>>
>
>
