dMRI preprocessing eddy_correct

dmri
nipype
neuroimaging

#1

Hello all,

I realised that my last post was a bit wordy. To summarise:

How can I use nipype to correct for eddy currents and also rotate my bvecs file accordingly, considering that I have not acquired a phase map and only have a single b0 volume?

Thanks in advance,
Joe


#2

Hi,
please have a look at:
http://nipype.readthedocs.io/en/latest/interfaces/generated/workflows.dmri/fsl.artifacts.html

I would use the all_fmb_pipeline. A zero filled dummy phase map will skip the SDC. The bmap_mag is only needed for registration and masking. The B0 image should do the job.

Joerg


#3

Thanks, I will give this ago using a dummy filled Phase file. How should I format the epi_param.txt file? I cannot seem to find any documentation for this.

Joe


#4

It’s a dict:

{
“delta_te”: 0.0023,
“echospacing”: 0.0007002373741777034,
“enc_dir”: “y”,
“acc_factor”: 1,
“epi_factor”: 128,
“epi_acc”: 1,
“epi_lines”: 55,
“field_axis”: “z”,
“field_strength”: 3.0
}