Hi. I am new to the forum, so I’m not sure this is the best way to post my question - but it would seem to be best related to this topic.
We have collected single shell data, 32 direction data (first acquisition is b=0, plus three additional b~= 0 interspersed within the b=1000 scans - they can’t be exactly zero, that’s a Philips limitation) with PA and AP data collected for all directions (separate scans on a Philips 3T Elition). My processing stream is as follows:
mrconvert each scan
dwidenoise each scan
mrcat the two scans
dwipreproc as follows:
dwipreproc DTI_combined.mif DTI_combined_EddyCorrected.mif -rpe_all -pe_dir PA -readout_time 0.0528 -eddy_options " --repol --acqp=AcqParameters_1acq.txt --index=indexFile.txt -export grad fsl --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear --mporder=6 --slspec=SliceOrder_MB3.txt"
where the file AcqParameters_1acq.txt has two lines for positive and negative PE, as follows:
0 1 0 0.0528
0 -1 0 0.0528,
and indexFile.txt is a string of 36 1’s and then 36 2’s.
What I don’t understand is that it seems to be running topup on the b=0 images only (topup_in.nii has 8 volumes), even though we have specified -rpe_all.
One thing I noticed is that the first b=0 image has been placed at the very end. I am pretty sure this is a Philips convention, but I am wondering if this is somehow overriding the rpe_all option.
Any thoughts/advice about this would be most appreciated! Thanks.
Mark Wagshul