Making Sure that the SDC has well-Applied

7

@jsein Thank you so much again for your time and the detailed guidance.

I have applied SDC using fMRIPrep LTS v20.2.7 as suggested, the output looks pretty reasonable.

SDC_LTSv20.2.7
SDC_LTSv20.2.71920×883 133 KB

I checked the fieldmap less SDC by including --use-syn-sdc flag with both v23.0.1 and v20.2.7_LTS. It did work fine to some extent for v.20.2.7 but not good for v23.0.1. The outputs are as follows:
synsdc with LTS v20.2.7

synsdc_LTS20.2.7
synsdc_LTS20.2.71920×881 134 KB

synsdc with v23.0.1

synsdc_v23.0.1
synsdc_v23.0.11920×875 146 KB

I started skullstripping the phasediff image using SynthStrip, but I’m having some trouble navigating it on singularity and HPC. I will try that and will upload the output here once created. (I intend to fix the issue by skull stripping the phasediff as suggested, to be able to use the latest fMRIPrep version).

Many thanks,
Ali

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