You can do it that way. You can remove the step of mapping the data into the volume and just pass the native volume to vol2surf and the bbreg registration as the --reg file (instead of --regheader). For mri_segstats, you can spec --avgwfvol lh.fmri_aparc.nii.gz (also I would add --excludeid 0 so that it does not report the medial wall as the 35th ROI). Once you have thatnii.gz as output for each subject, you canrun mri_concat to concatenate all of them together. Alternatively, if you want a text file matrix as output, you can use --avgwf file.dat, then just cat the file.dat for each subject into a single file

On 05/19/2017 11:52 AM, Elijah Mak wrote:

Hello Freesurfer Experts,

I have a question to ask about extracting the mean time series from resting-state fMRI (239 volumes).

I have used bbregister to bring the 4D fMRI data into T1 space. My next objective is to project the data onto the fsaverage surface, and then extract the mean time series for each ROI.

These are my steps so far. Can anyone let me know if I am on the right/wrong track?

bbregister --s $i --mov ${i}_medn.nii (fMRI resting-state) --init-fsl --t2 --reg ${i}/fmri/fmri_t1.dat --o ${i}/fmri/fmri_t1.mgz

mri_vol2surf --src ${i}/fmri/fmri_t1.mgz --out ${i}/surf/lh.fmri.mgh --hemi lh --projfrac 0.5 --interp nearest --regheader ${i} --trgsubject fsaverage

mri_segstats --i ${i}/surf/lh.fmri.mgh --annot fsaverage lh aparc --sum ${i}/stats/lh.fmri_aparc.sum

Ultimately, how may I derive a 239 (volumes) x 34 (ROIs per hemisphere) matrix of the data?

Appreciate your help. Thanks!

Best Wishes, Elijah

*Elijah Mak, Research Associate* Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK

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