[Freesurfer] activation timeseries

Dear Freesurfer experts

I want to extract "activation timeseries (BOLD signal changes in each time point) " from a predefined ROI in a single subject task fMRI data. Previously, I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats, but the data seems to be too noisy. I searched the forum and found this solution (mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat This will detrend the time series (removing mean, linear, and quadratic

trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended time series). If you have a task, the task will still be in there.https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18901.html

I ran this command: mri_glmfit --y fmcpr.nii.gz --qa --glmdir qa.glm --save-yhat and then this command to extract the timeseries: mri_segstats --i yhat.mgh --slabel arap_7T_all lh $SUBJECTS_DIR/arap_7T_all/lh.label --id 1 --avgwf-remove-mean --avgwf ./lh.01.txt I got this error: ERROR: dimension mismatch between input volume and seg input 174 174 51 seg 148565 1 1 I would like to know if this is the right way to extract timeseries from a task data. and if yes, how can I fix the error.

Thanks a lot Mona

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129