I am newly working on diffusion MRI, but I have some question about the data dimension, here is the problem:
Yooo, mec, I run one PREVDEMALS subject for FREESURFER diffusion pipeline, so I found a interesting question and got some interesting result about the bvec/bval and dwi.nii dimension problems.
Basically, in my dataset, all the dwi imges(.dwi.nii.gz), they have 137 volumes/nFrames during the session, and the bvec/bval have 136 columns(nFrames-1), this works well for Nipype(Mrtrix and Dipy) pipelines, but when i run it in TRACULA, it complains the error that the data and the bvec/bval dont have the same entries, which makes sense, So I found information for Freesurfer, it is said that
'The bvalues are in a simple text file, one for each direction
(including b=0). The bvectors (gradient directions) are also in a
simple text file with three components on each row. These also include
the b=0 values. There must be as many rows in the bvals/bvecs
as there are frames in the input’
So to avoid the error, I just add 0 for the first column for bvec and bval, the pipeline run without errors, but when I check out the the outputs, I found that for the fractional anisotropy(fa.nii), it is not right, some high values bigger thatn 1, which is impossible, So I guess the problem is that its the adding 0s.
So my question is that, when define the bvec and bval, why the dimension is nFrames-1, but Freesurfer requires the same dimensions??
BTW, my data is in the BIDS specification.
Really need your help:)