Hi all, using dwipreproc RC1-44, also for topup. Have dMRI full data in AP (e.g. 10x b0 & multishell bXXX data) and reverse phase b0 data (e.g. 5x b0 & no bXXX data). Before I used something like: dwipreproc -cuda -rpe_pair DTI_b0_AP.mif DTI_b0_PA.mif -force -nthreads $ncpu AP DTI_dn.mif DTI_dn_…

Hi Stefan, It’s a good question. There is indeed nothing preventing you from using all AP-PA images for field map estimation, and topup allows you to do this easily. The dwipreproc script is designed as a simple wrapper around topup and eddy to deal with the most common use cases. We never intended…

Thx @dchristiaens , doing an average of all AP and PA b0 now. But keeping in mind your consideration about large bulk head motion… Groetjes, S.

Hi Stefan, I might initially go on a bit of a tangent on this one; I promise it’ll come around to answer the question, but I’m hoping it’ll give anyone curious a better understanding of how I made this all work. With 3.0_RC1, dwipreproc has been basically re-written from scratch, largely due to th…

Hi @rsmith , Rob, I’ll look into the -rpe_header option. At present working with GE and Philips data. Concerning: “assuming you have a Siemens scanner and don’t use any non-MRtrix3 commands between DICOM import and dwipreproc invocation”, and being lazy, and not (yet) reading the source code, how …

Currently it reads 0018 1312 and a couple of Siemens CSA entries . Should absolutely be possible to import from other vendors, but I only have access to Siemens data and so have not had the information necessary to configure the import for data from other vendors. If anybody can get me data on the ap…

Dear Rob I have a data set from Philips which I think (and would appreciate if you can also confirm) has different readout times for rev (3 vols) and dwis (102 vols). So I was wondering whether it is possible to pass different readout times to dwipreproc using -read_time option? Please let me kno…

Hamed, No, you can’t manually specify different readout times for different volumes. dwipreproc's only purpose for existence is to simplify the interaction with FSL’s topup and eddy tools in the most common use cases; if the command-line interface were sufficiently complex to handle any arbitrary a…

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Dwipreproc -rpe_pair: Why equal number of up/down b0 encodings?

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