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 51seg 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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