I want to project the region of interest (ROIs) from [1] on my subjects' surface and create a NIFTI file out of them. The ROIs are in 1d.dset format in AFNI. To do this, first, I mapped ROIs (e.g. v1_lh.1d.dset) on the subject surface (std.141.mysubj_lh.spec), which has been created in Freesurfer and converted to spec file using @SUMA_Make_Spec_FS, with the following command:

3dSurf2Vol -spec std.141.mysubj_lh.spec -surf_A lh.smoothwm -surf_B lh.pial -grid_parent mysubj_SurfVol.nii -sv mysubj_SurfVol.nii -map_func ave -f_steps 10 -f_index voxels -sdata_1D v1_lh.1d.dset -prefix v1_lh.nii.gz

The result was acceptable (figure below).

I want to align the NIFTI files from ROIs (e.g. v1_lh.nii.gz) with the EPI images. However, the structural image from @SUMA_Make_Spec_FS is not aligned with the EPI image. Would you please help me to align the masks (ROIs) with the EPI image?

* One solution that comes to my mind is to align the structural image with the EPI image using align_epi_anat.py. Then use the transformation matrix form align_epi_anat.py to align masks with the EPI image, but I do not know how to use the transformation matrix to transform the masks.

[1] Probabilistic Maps of Visual Topography in Human Cortex; Liang Wang, Ryan E B Mruczek, Michael J Arcaro, Sabine Kastner