Resampling glitch when the NiFTI header is oblique

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This topic contains 3 replies, has 2 voices, and was last updated by  robreid 3 months ago.

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  • #1263

    robreid
    Participant

    Hi,

    I noticed a resampling glitch when the dMRI is warped to a T1 with an oblique sform:
    Resampling glitch

    The glitch appears as one or more diagonal fault planes that are more or less conspicuous depending on the local contrast – the screenshot shown is from the worst case on the inferior edge of the CC.

    The T1’s sform is
    srow_x 280 4 1.195487 -0.00832 -0.0876 -85.916519
    srow_y 296 4 0.029844 0.995965 0.197129 -165.741318
    srow_z 312 4 0.099596 -0.198567 0.992426 -124.586205

    There is no problem when the same T1 is used with sform
    srow_x 280 4 1.2 0.0 0.0 -99.663498
    srow_y 296 4 0.0 1.0156 0.0 -97.173988
    srow_z 312 4 0.0 0.0 1.0156 -128.981201

    Has anyone else seen similar problems with obliqued T1s, and is there a possibility of fixing the resampler?

    Thanks,

    Rob

  • #1264

    robreid
    Participant

    It does not look like the img button worked; try https://photos.app.goo.gl/PJyZ5xz0iQlfiGJi2 or email me.

  • #1299

    Anand Joshi
    Moderator

    Hi Rob,
    Thanks for reporting the issue. Can you please let me know which executable were you using? Was it BDP.sh?
    You can try the following workaround for now. You can simply load and save the T1 from brainsuite. It should save the header in brainsuite friendly format. Then proceed with the analysis using this saved T1.
    Anand

  • #1331

    robreid
    Participant

    Hi Anand,

    Sorry for not replying earlier. I was using BDP.sh, for scriptability, and have never actually gotten the whole brainsuite package running. If I understand correctly though, and I think I do, I could easily manipulate the T1 to have a diagonal (non-oblique) affine matrix outside brainsuite, and carry on. I do not mind resampling the T1 for this purpose since its native resolution is much better than the dMRI’s.

    Thanks!

    Rob

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