Clarify the "fs-no-reconall" command

1

Hi,

I just wanted to clarify two things about the “–fs-no-reconall” argument for fMRIprep.

We are rerunning a series of scans where we want to reuse the previously run freesurfer data. We are already pointing the preprocessing to the old freesurfer data “-fs-subjects-dir” argument.

  1. does adding the “no-recon-all” step actually save any time?

  2. will adding it when already pointing to the previously run freesurfer data affect the functional scans?
    In other words, are there any differences between functional MRI preprocessing pipeline that DOES and DOES NOT have this “–fs-no-reconall” command included assuming we are using freesurfer data that was previously run without this command. I notice when this command is included in the preprocessing it doesn’t output the surface reconstruction stuff in the .html file which is probably ok as long as it doesn’t affect any of the functional preprocessing output.

See discussion below which I think touched on this. Sorry, I just want to clarify that we are doing this correctly. fMRIPrep --fs-no-reconall / re-running preprocessing

2

Hi @AustinBipolar,

Yes but not for good reasons. The fs-no-recon-all step will disable further downstream surface level steps, like boundary based registration, which you should want to keep. The volumetric analogs may be quicker, but generally do not perform as well.

Yes, for the same reason stated above.

In short, do not use --fs-no-reconall.

Best,
Steven

3

Thanks as always for the quick respond. I really appreciate it.