Odd boundaries in LN2_PHASE_JOLT outputs

Software Support
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Summary of what happened:

I am trying out laynii’s LN2_PHASE_JOLT on low-resolution multi-echo fMRI data (2 mm isotropic voxels), and I noticed that there are hard boundaries in the resulting phase jump/jolt images. I’m wondering if this is a known issue in these derivatives, or if I need to do some processing first. I was under the impression that phase unwrapping was unnecessary for phase jump/jolt calculation, but if necessary I can do that first.

Command used (and if a helper script was used, a link to the helper script or the command generated):

LN2_PHASE_JOLT \
    -input $echo_file \
    -int13 \
    -phase_jump \
    -2D \
    -output $out_prefix

Version:

v2.8.0

Environment (Docker, Singularity / Apptainer, custom installation):

Linux64 distribution. No container.

Data formatted according to a validatable standard? Please provide the output of the validator:

n/a

Relevant log outputs (up to 20 lines):

n/a

Screenshots / relevant information:

Phase jump

jump
jump824×832 22 KB

Phase jolt

jolt
jolt824×832 23.4 KB

1 Like
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Hi @tsalo ,

Could you let me know what is the range of the values in your input nifti? Eg are they between 0-4095, or -pi to pi, or something else?

When these hard edges occur, it is often due to discrepancy between the input values and the programs setup/parameters. You do not need to unwrap first, thats the whole point of this program as the unwrapping in handled during derivative computation across voxel pairs through circular subtraction.

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The values are between 0 and 4094. The only processing I’ve done is to split no-excitation-pulse volumes out of the end of the run with nibabel, which might have changed the intercept and slope in the NIfTI. (The contents are still fine though)

The sequence is 2D, but I did notice that the -2D flag was experimental. Could that be the problem?

1 Like
4

Hmm, it might be that you have a non standard 2D axis, or the slope and intercept indeed can cause trouble. I think this might need to be solved by me looking into your input nifti carefully.

Do you mind sending me an example nifti? Either though here or LayNii issues on github?

1 Like