The IXI dataset openly provides scans of diffusion MRI from a large number of subjects. There is however a strange discrepancy in the data. The b-vectors and b-values that are provided have 16 entries each. This includes a zero entry in the b-values, which corresponds to the first volume of the acquisition. The first b-vector is [0, 0, 1], but there is also a [0, 0, -1] in the table further down, so I suspect that this is also supposed to be zero. However, there are 17 volumes of diffusion data provided. They are provided as 17 different nifti files, named “XXX-DTI-00.nii.gz”, “XXX-DTI-01.nii.gz”… “XXX-DTI-16.nii.gz”, where “XXX” is the individual subject identifier – something like “IXI640-Guys-1106”.
In the past when I analyzed this data, I scratched my head, tried a couple of things and then came to the conclusion that dropping the last volume makes sense. This was done based on looking at FA, MD and color FA maps for a few individuals and based on the fact that dropping that volume results in the best model fit for the DTI model. But now I am wondering whether anyone out there knows what is actually going on here.
Why are there 17 volumes in this data, but only 16 b-values/b-vectors? If the last volume really shouldn’t be used for fitting the data, what is that last volume for?
Aha! Upon further inspection (and with thanks to Jason Yeatman for suggesting this!), it seems that this last volume is the mean diffusivity or trace, or some-such. In other words, if you want to analyze the data from scratch, dropping that last volume is sensible.
As you said above I drop the last volume according to strange discrepancy in the data about number of volume and contents of bval and bvec files, but in this situation I have this error in ExploreDTI software :
Error loading ‘E:\IXI002_DTI\no16\IXI002.txt’: the number of rows in this file (here, 16) should be equal to the 4th dimension of the diffusion data (here, 15) … skipping data set!
Cannot open file C:\Program Files\Polyspace\R2019a\bin\Source\Settings\Data_conv_wi.txt.
Perhaps adding ‘write’ permissions to file ‘Data_conv_wi.txt’ will solve this error…
and I add write permission to that file as well but this error remained. It means that removing that volume would not be the solution. I would be so gratefull if anyone help me to solve this problem.
Thanks in advance and looking forward to hearing from you.
Thanks for posting this. Unfortunately, I am not really familiar with ExploreDTI, so I am not entirely sure what’s going on. Maybe someone else here knows more…
That said, I did notice that the error mentions that the data you are analyzing now only has 15 volumes. Are you sure you only dropped the last volume from the 4D image? Is it possible that you dropped one more along the way?
Thank you for your consideration and time.
I don’t know why that error occur, because I just drop the 17th image and after that transfer them to 4D by FSL (through fslmerge command).