Revisting --fs-no-reconall

[Jon_Brooks]

Hi,

I understand that turning freesurfer recon off in fmriprep may lead to less accurate registration of EPI to T1 structural data as boundary based registration (BBR) is not used. Has anyone compared the results from this “fmriprep:BBR” to BBR as implemented in FSL? I guess one significant difference would be the approach taken to find the grey/white matter boundary - FAST vs freesurfer.

As a related question, if I do use freesurfer recon, and have fmriprep do all the heavy lifting for EPI → T1 structural → standard brain registration, is there a way to take the generated transforms/warps and build a “reg” folder that would keep FSL happy?

For various reasons I have to keep the functional data in “func” space for the purpose of processing (tedana, 1st level FEAT), but would then like to take advantage of fmriprep’s registration pipeline when performing group analysis.

Sorry for the slightly vague questions, if someone can point me in the right direction I’d be most grateful.

Best wishes,
Jon

[Steven]

Hi @Jon_Brooks,

@Jon_Brooks

Has anyone compared the results from this “fmriprep:BBR” to BBR as implemented in FSL? I guess one significant difference would be the approach taken to find the grey/white matter boundary - FAST vs freesurfer.

Not explicitly, as far as I know. But empirically surfaces from FreeSurfer tend to look better than those from any volumetric workflow. For example, the difference between MRtrix’s 5ttgen (5ttgen — MRtrix3 3.0 documentation
) for the fsl (no surface data) and hsvs (uses freesurfer) options is pretty significant.

@Jon_Brooks

For various reasons I have to keep the functional data in “func” space for the purpose of processing (tedana, 1st level FEAT)

You can just have a func output space in fmriprep: Defining standard and nonstandard spaces where data will be resampled — fmriprep version documentation

Best,
Steven