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August 08, 2019 09:58AM
Hello everyone,

I am trying to align my anatomical to my functional however I am getting very poor results for some participants (see attached images). After alignment the anatomical looks very wonky and this was happening on quite a few participants. I have tried using different cost functions such as lpa and nmi but have had no luck. When I try the alignment on another computer with an older version of afni the alignment looks good.

Computer 1 (mis-aligned): Afni version: 19.2, AMD chipset, Ubuntu 18.04
Computer 2 (well-aligned): Afni version 18.3, Intel Chipset, MacOS High Sierra

Here is the command I was using: -overwrite -anat2epi -anat MPRAGE1.nii \
-suffix test_al \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc+ZZ \
-volreg off -tshift off

Thanks for any help,

Naail Khan

Subject Author Posted

Significantly mis-aligned data from Attachments

naailk90 August 08, 2019 09:58AM

Re: Significantly mis-aligned data from

Daniel Glen August 08, 2019 05:51PM

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