Hi Bruce,

Thank you for the reply! I have now tried:

mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh --tal --talres 2

mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal --talres 2

mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz

mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz

mri_convert masked_fmri.mgz masked_fmri.nii

I got:

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from masked_fmri.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to masked_fmri.nii...

However, when I opened the masked_fmri.nii in fslview, the masked_fmri seems to be empty (intensity is zero and no brain is shown).

I would need to get a matrix containing voxels in the grey matter at all time points. Could you please let me know what I am doing wrong above? Or is there some better way to do this? I am new with Freesurfer, so sorry if my questions are trivial.

Best,

Maria