Hi Mona, I'm not sure what you are trying to do here. Using a different program is not going to make your data less noisy. The mri_glmfit command will remove mean, etc, but you are running it on fmc.nii.gz which is in the native functional space. If this is what you want to do, then run it on fmcpr.sm0.self.lh.nii.gz then run mri_segstats
doug

On 2/4/2020 9:59 AM, Nasiriavanaki, Zahra wrote:

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
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