Hello,
we want to estimate the orientation of the fibers in each voxel with constrained spherical deconvolution using Mrtrix. At the beginning, we would like to use files from AutoQc (e.g., *AutoQCed_DWI.nrrd), however, we could not convert the NRRD data to Nifti using 3D Slicer. We then choose to preprocess the origion data using mrtrix, which need to provide the phase encoding direction of these DWI datas. So would you please provide the phase encoding direction of these data for us.
Thanks.
The diffusion data was not acquired with a dual polarity encoding, but twice refocused acquisition, and thus there is only a single DWI acquired without polarity encoding. I.e., it does not have phase encoding directions that you can enter in mrtrix's preprocessing. You probably could try to enter any polarity encoding information. But the issue is that it will aim to correct distortions in that encoding direction, which might yield less than optimal results.
Hi, many thanks for your reply. if I don't use fsl or mrtrix3 to do eddy correction, but use DIPY for motion correction between volumes, is this okay?
Motion correction in dipy is probably fine (I have not used it before, so I have limited experience with it), you need to make sure it does also eddy current correction (which is commonly performed in the same step as motion correction via estimating an affine registration). We are either using our own implementation or the one in fsl's eddy.
Martin
Hi, Martin
Thanks for the reply! As I am kind of new in DWI analysis, I have some quetions about these data, and apologize in advance for the following questions.
1. I noticed the orientation of the raw DWI data differs
from the processed data, so I reoriented the raw data using 3D
Slicer and fslswapdim before preprocessing. However, I'm not sure
if this method alters the bvecs. If so, is there a better way to
reorient the data (the same orientation with the processed T1
images) and output the corresponding bvecs?
2. When using FSL's eddy for Eddy Current Correction, is it
reasonable to set the parameter of acqp.txt to -1 0 0 0.1 (since
there is no phase encoding direction, I arbitrarily chose one
direction).
Best,
Ruilin Tu
Reorientation of DWI data can indeed be an issue when bvecs are not correctly updated. I suggest you use one of the existing DWI tool datasets to process your data, as these tools know how to correctly adjust bvecs. Btw, if you have a re-orientation transform matrix and you apply it in Slicer via its resampling tool, the gradient vectors will get correctly updated if you have the DWI data as NRRD (I am not sure, but I doubt that Slicer is doing it correctly for nii/bvec/bval data).
Re eddy: Likely it does not matter, given you do not provide eddy with any information from topup.
Originally posted by tu ruilin:
Hi, Martin
Thanks for the reply! As I am kind of new in DWI analysis, I have some quetions about these data, and apologize in advance for the following questions.
1. I noticed the orientation of the raw DWI data differs from the processed data, so I reoriented the raw data using 3D Slicer and fslswapdim before preprocessing. However, I'm not sure if this method alters the bvecs. If so, is there a better way to reorient the data (the same orientation with the processed T1 images) and output the corresponding bvecs?
2. When using FSL's eddy for Eddy Current Correction, is it reasonable to set the parameter of acqp.txt to -1 0 0 0.1 (since there is no phase encoding direction, I arbitrarily chose one direction).
Best,
Ruilin Tu