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Dear Ting-Yu, Many thanks that you are codisering my problem. I am going to run TOPUP using your suggestion. I'd like to ask what "unusually noisy" is in my data. Is it because we scan the monkey with small FOV and the resolution of 1mm? yes, this is in no way a value judgement. It simply reflects that the voxelwise SNR is lower than I am used to seeing. Which makes complete sense since I am used to seeing data acquired on larger brains and larger voxels. Do you have any idea to reduce the noise and improve the quality of my scanning? Any advice and suggestions will be greatly appreciated. I am afraid I don’t know enough details to be able to answer that. My guess is that this is simply a consequence of small object and high resolution. It is not a problem for topup per se, it was just that it seems to have revealed a behaviour that I hadn’t thought could happen. I expect the new configuration file to fix that for you. Jesper Thank you so much, Ting-Yu On Tue, Nov 1, 2016 at 9:54 AM, Jesper Andersson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Ting-Yu, I can repeat your problem, and I kind of understand why it is happening. Though it is still quite surprising to me. The regularisation that is applied to the field inside topup is applied to the (estimated) off-resonance field. If you increase your readout-time by a factor of ~15 (0.065 to 1) you effectively increase the magnitude of the off-resonance field by the same factor, and hence you also increase the regularisation by a factor of 15. The reason it is still surprising to me is because the b02b0.cnf effectively turn down the regularisation by each subsampling-step such that at the end it is more or less zero. This is why I usually say that it doesn’t matter what you put in the last column, and on all data sets I have seen in the past this has been true. However, it seems in your case that it does make a difference. It seems that already in the very first iterations it takes much smaller steps for the 0.065 readout than for the 1 readout. My best guess as to why we see this behaviour in your data, and not in other data, is because your data is unusually noisy and hence regularisation plays a greater role. For now, if you wish to use the correct readout of 0.065, I suggest you divide each value on the row --lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001 by 15. I.e. make it --lambda=0.00033,0.000067,0.0000067,0.000001,0.00000033,0.000000033,0.0000000033,0.000000000033,0.00000000000067 and maybe also increase the number of iterations. I have enclosed a modified b02b0.cnf. This issue is something that I will have to revisit when I have more time. Jesper On 26 Oct 2016, at 16:23, Ting-Yu Chang <[log in to unmask]<mailto:[log in to unmask]>> wrote: 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]<mailto:[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 On Thu, Oct 20, 2016 at 4:37 AM, Jesper Andersson <[log in to unmask]<mailto:[log in to unmask]>> 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 https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5<https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F> 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-Madison Physiology Graduate Training Program 1-608-335-1628 [log in to unmask]<mailto:[log in to unmask]> 張廷宇 +886-919-058-196<tel:%2B886-919-058-196> [log in to unmask]<mailto:[log in to unmask]> -- -- Ting-Yu Chang University of Wisconsin-Madison Physiology Graduate Training Program 1-608-335-1628 [log in to unmask]<mailto:[log in to unmask]> [log in to unmask]<mailto:[log in to unmask]> -- -- Ting-Yu Chang University of Wisconsin-Madison Physiology Graduate Training Program 1-608-335-1628 [log in to unmask]<mailto:[log in to unmask]> [log in to unmask]<mailto:[log in to unmask]>