How do I calculate --acqp?

For t1 structural data, there is an option in VBM 8 to preprocess longitudinal data- whereby each image is registered to a subject's mean image across time points. I cant find any similar or equivalent option for FSL TBSS. I wonder if anyone has figured out a way to do this?

Hi everyone,

There are some articles about this issue, but methods section are not clear enough explaining how they have corrected this (i.e., free water elimination).

Thanks in advance!

J

I'm running Tracula. I already computed most of the pre-processing while processing my DTI data using FSL. Do I need to do all of this again for Tracula?

(Eddy-current correction, registration, dtifit but NOT Computing anatomical priors for WM pathways from training data) + Bedpost + recon

Dear all

Few questions about whole brain tractography and template based network analysis on ExploreDTI.

1 - Could I normalize my diffusion image to perform the whole brain tractography? I understand that this may introduce errors, but how can I use a template as AAL to create a connectivity matrix on native space? Deformation field transformation introduce new indices to the Atlas (due the interpolation) so, the deformed image have more indices than the Label text file, as expected.

2 - How can I actually get a connectivity matrix after perform the network analysis (at this point with normalized DTI and AAL template).

3 - Should I add both directions of the pair of ROIs? (e.g.: [L Hippo - L Amygdala] and [L Amygdala -L Hippo])?

Thank you very much!

Hi Guys, 

what is the difference between both given that both can be used to correct distortions?? 

I understand the FUGUE is a set of tools for EPI distortion correction, so is it right to say that TOPUP is a subset of FUGUE?

Many thanks for the help!

-Newbie at DTI

Because the documentation says that you need a P>>A and A>>P directions but I only have one of them.

Hi there, wonder if someone could help me out

We obtained EPI images in a GE MR scanner with opposite phase encoding direction in order to construct a B0 inhomogeneity fieldmap using the topup command in FSL. The problem is that the fieldmaps obtained show some kind of artifact represented by vertical lines in the phase encoding direction (A-P).

Does anyone know why these artifact is observed and how to prevent or correct it?

I appreciate your kind help.