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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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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