I am updating a pipeline using the latest stable (302) mrtrix3 version.
As input, I have 4 dwi vols sets/subject:
set 1: 10Xb0, 60 dirXb700 (70 vols total), pe dir: j-
set 2: 10Xb0, 60 dirXb700 (70 vols total), pe dir: j
set 3: 10Xb0, 60 dirXb3000 (70 vols total), pe dir: j-
set 4: 10Xb0, 60 dirXb3000 (70 vols total), pe dir: j
sets 1,2: TE: 0.083, TR 8.02
sets 3,4: TE 0.11, TR 9.65
sets 1-4: readout 0.0508
All preceding preprocessing in the pipeline (from dicom import on) is via mrtrix3. Sets 1-4 are concatenated in an input vol predwi_denoised.mif. With dwifslpreproc, I want to account for both intraset and in-between set aquisition motion, and eddy to topup correlation, and I was thinking of the following command:
dwifslpreproc predwi_denoised.mif dwi_preprocessed.mif -rpe_header -align_seepi -eddy_options " --mporder=#" -readout_time 0.0508
I would appreciate your assist with:
I see with verbose that the command extracts a se_epi.mif volume with b0 vols, so I assume I do not need to feed the -se_epi option if using -align_seepi, is this true
in the dwifslpreproc command description, if I am correct, it is mentioned that the use of -align_seepi requires se_epi.mif and the other imput (predwi_denoised.mif) to have the same TE, TR. Given the different TE, TRs in between sets 1/2 and 3/4, respectively, how can one use this option properly?