Fmriprep recon-all with multiple sessions T1w and T2w

jsein · June 30, 2023, 11:38am

Hi Cesar, could you specify which fmriprep version are you working with?

With multiple T1w images, they are several ways that fmriprep can process them with help of freesurfer:
Some details are here:

github.com/nipreps/fmriprep

DOC: Indicate that 2 T1w images are not merged to an unbiased template

opened 08:59PM - 26 Oct 22 UTC

closed 07:29PM - 07 Dec 22 UTC

effigies

documentation

Following https://neurostars.org/t/specify-anatomic-image/23853/9, it seems our …docs are inaccurate. > In the case of multiple T1w images (across sessions and/or runs), T1w images are merged into a single template image using FreeSurfer’s [mri_robust_template](https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template). This template may be unbiased , or equidistant from all source images, or aligned to the first image (determined lexicographically by session label). For two images, the additional cost of estimating an unbiased template is trivial and is the default behavior, but, for greater than two images, the cost can be a slowdown of an order of magnitude. Therefore, in the case of three or more images, fMRIPrep constructs templates aligned to the first image, unless passed the --longitudinal flag, which forces the estimation of an unbiased template. This seems to indicate that we make an unbiased template for two images but not three or more. In fact, we always use `--fixtp` unless `--longitudinal` is set.

And the updated FMRIPREP description is here:

About the T2 images, there is this information from @effigies :

I hope this helps!