Hi Jesper,
Could you please help us to check the data that I have uploaded last week? I can't still figure out my issue.
Thanks in advance,
Ting-Yu
On Thu, Oct 20, 2016 at 12:27 PM, Ting-Yu Chang <[log in to unmask]> wrote:
Dear Jesper,Thanks for your reply. I have uploaded the file, DTI_for_Jesper_fromTingYu.tar. Please check if the files are available. I'd like to mention that the data is obtained from the monkey in sphinx position.
The commands I used are as follows:
fslmerge -a DTI_pe0_pe1_b0_01.nii.gz DTI_pe0_b0_1.nii.gz DTI_pe1_b0_1.nii.gz
topup --imain=DTI_pe0_pe1_b0_01.nii.gz --datain=acqparams.txt --config=b02b0.cnf --out=topup_results --fout=topup_field --iout=topup_unwarped
topup --imain=DTI_pe0_pe1_b0_01.nii.gz --datain=acqparams_0p065.txt --config=b02b0.cnf --out=topup_results_65col --fout=topup_field_65col --iout=topup_unwarped_65col
Best,
Ting-Yu
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On Thu, Oct 20, 2016 at 4:37 AM, Jesper Andersson <[log in to unmask]uk> wrote:
Dear Ting-Yu,
After searching and looking this forum, I am still confused about the fourth column of the parameter for TOPUP.
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1607&L=FSL &D=0&1=FSL&9=A&J=on&d=No+Match %3BMatch%3BMatches&z=4&P=59667
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=FSL &D=0&P=317857
Two acquisitions are obtained with the opposite phase directions from the GE scanner. The effective echo spacing is 1.024 ms, the ASSET factor for parallel imaging is 2, and the acquisition matrix is 128*128. For my understanding, the dwelling time is effective echo spacing/ASSET factor = 1.024/2 = 0.512 (ms). The readout time can be calculated from the actual echo spacing (the dwelling time) multiplied by (acquisition matrix - 1). The readout time = 0.512 * (128-1) * 10^-3 = 0.065 (s).
I used this value as the fourth column in the acqparameter.txt as running TOPUP. Please check the links as follows.
1. set to 1: https://drive.google.com/file/d/0B5HVOqozGjskREtNdlBVdGlIN3c /view?usp=sharing
2. set to 0.065: https://drive.google.com/file/d/0B5HVOqozGjskSlVQOVF3bHc3VGM /view?usp=sharing
The screenshots are the unwarped result from theTOPUP as the fourth column of the parameter set as 1 and 0.065. You can see the result from the value 1 shows less distortion than that from the correct value, 0.065. I am so confused because Jesper mentioned the fourth column would no affect the result so that we can use any vaules, like 0.05, to run topup+eddy. Why do we have different warped result from topup?
I am equally confused as you about this. I have never seen anything but completely non-significant differences between topup runs with different readout-times.
If you tar your inputs to topup into a single file and upload it to
and send me your exact topup command line in a mail I will see if I can find an explanation.
Jesper
Could you please help me to figure out these questions? I am a beginner for MRI. Any suggestion will be helpful.
Thanks,
Ting-Yu
--Ting-Yu Chang
University of Wisconsin-MadisonPhysiology Graduate Training Program1-608-335-1628張廷宇
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--Ting-Yu Chang
University of Wisconsin-MadisonPhysiology Graduate Training Program1-608-335-1628