In fsfast, the censoring is done in the analysis by creating a tpexclude file and specifying this file when running mkanalysis-sess. Below is a snippet from the mkanalysis-sess --help

-tpexclude tpxfilename

This is the name of a time point exclude file (TPEF) used for removing outliers in the time series. The TPEF stores a list of times (in seconds) of time points to exclude from the analysis. The TPEF must be found in the run directory with the functional data to which it applies. Like paradigm files, the TPEFs must have the same name across subjects and runs though their contents can differ.  Unlike paradigm files, it is not necessary to have a TPEF in each run; if no TPEF is found, no time points are excluded.

On 6/11/2024 12:58 PM, Possidente, Thomas wrote:

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Hi there,

I’m using this version of Freesurfer: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460

I’m using mc-sess to run motion correction on some functional task and resting state data. I would like to perform censoring on high motion timepoints in order to reduce spurious correlations due to movement during connectivity analysis. My main question is: does mc-sess include censoring? If so, what are the threshold parameters? If not, are there any optional arguments to turn censoring on? If not, how do you recommend doing motion correction with censoring using Freesurfer? I know mc-sess uses AFNI’s motion correction, just not sure if it utilizes censoring.

Thank you,

Tom

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