Dear All,
These are rookie questions to optimize dwipreproc output.
I have two sets acquired sequentially within the same scan session (each set contains 10 Xb=0 images acquired first in the respective set, then 60 dwi b=700; 1st set (70 vols) AP, 2nd set (70 vols) PA encode direction, on SIemens Trio).
The expected dwipreproc output in this case is a 70-vol mif file (‘result.mif’). However, I get an 140-vol result mif. What happened? I inspected the gradient file, grad.b (generated by dwipreproc with dwgrad), which I attach at the end of the post, and I noted that for one (1, !) dicom/vol, the AP (vol no 11) and PA (vol no 81) do not have identical gradients (see the end of this post, mismatch highlighted).
I verified this is the case with another mrtrix tool
dcminfo -a -csa 11.dcm
and I got
[CSA] PhaseEncodingDirectionPositive: 0
[CSA] NumberOfImagesInMosaic: 64
[CSA] DiffusionGradientDirection: -0.99996662 0.00577977 0.00577977
and
dcminfo -a -csa 81.dcm
[CSA] PhaseEncodingDirectionPositive: 1
[CSA] NumberOfImagesInMosaic: 64
[CSA] DiffusionGradientDirection: -0.99996662 -0.00577977 0.00577977
-
I wanted to make sure this is a hardcoded header issue and not a reading error through mrtrix. If it’s a header issue, it could be a SIemens soft error in the grad table prior to scanning or a header imprimatur error after scanning. Have you seen these kind of mismatches, if so which is likely the cause?
-
Due to this mismatch (and a resulting no of image pairs less than half the total no of volumes), dwipreproc does not recombine any volume pairs, and as such the full complement (140 vol) of the AP-PA vols are present in the output.
As a strategy (with an eye to the subsequent tractography/connectome steps), should I a. leave it as is (140 unrecombined volumes, 2. throw the two vols wtih mismatched gradients, and obtain a recombined dwipreproc output with 68 vols?
Thank you,
Octavian
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