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I see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
On 4/2/19 4:23 PM, Zhi Li wrote:
External Email - Use CautionDear Freesurfer experts,
I would like to transform the task-based surface data to volume. May I know if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002 --so fs/sub002/surf/lh.white fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system frozen. Any suggestions would be appreciated.
You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002.
Another problem is that in some individuals I found the RAS information of preprocessed surface data of different sessions are not identical, that means the "voxel to ras transform" and "ras to voxel transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between seesion1 (folder 001) and session2 (folder 002). May I know how this happened and will it influence the final result? Should I keep them the same?
The vox2ras for surface overlay data is not valid, so ignore it.
Thanks,
LIzhi
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