Dear Jasper,
I have DWI data (The images were acquired using a single-shot, spin echo, and echoplanar imaging sequence with twice refocused spin echo diffusion preparation (Q-ball imaging). Each series included 60 images acquired with diffusion weighting and 8 noncollinear directions.
I ran eddy_correct and I calculated motion parameters and SNR. Motion is excessive!! in this data set, and as a result we need to exclude large number of my subjects (~60%) of the data. I am hopping that using "topup and eddy" to correct motion in this data set would help a bit. I did the following:
The raw dwi data is in the form of nifit "dwi.nii" is a longside with "bvals" and "bvecs" within a folder named "subj1"
cd subj1
fslroi dwi.nii nodif 0 8
gedit acqparams.txt
0 -1 0 0.0608991
0 -1 0 0.0608991
0 -1 0 0.0608991
0 -1 0 0.0608991
0 1 0 0.0608991
0 1 0 0.0608991
0 1 0 0.0608991
0 1 0 0.0608991
topup --imain=nodif.nii --datain=aqu --config=b02b0.cnf --out=my_topup_results
fslmaths nodif -Tmean nodif_mean
bet nodif nodif_brain -m
indx=""
for ((i=1; i<=68; i+=1)); do indx="$indx 1"; done
echo $indx > index.txt
eddy --imain=dwi.nii--mask=nodif_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results --out=eddy_corrected_data
Then I fed "eddy_corrected_data" to the following steps in the preprocessing pipeline for DTI data in FSL
Kindly, I have the following questions:
1. Are the previous steps correct?
2. Regarding "acqparams.txt". Is it correct for my DTI data ( acquired as mentioned above) to extract all the non-diffusion volumes then create a text file (8 lines one for every b0). The order of the negative and positive values is as above? Is there any difference in the order of the volumes in this file ( I mean adding negatives first or positives first)?
3. In the file "acqparams.txt" what are 0 1 0 stands for? are these numbers the same in all types of DWI data
4. Is it correct to feed the output of topup directly to eddy or I need to run the command "applytopup " following "topup" and then feed the output of "applytopup" to eddy?
Thank you very much for any advice
All the best,
Jon
|