I have created an ROI from regions V3A and V3B. I have also converted the resulting surface ROI to a dset file using the following:
ROI2dataset -prefix 7T_V3A_V3B_mask_v2.niml.dset -input 7T_V3A_V3B_mask.niml.roi
however, when I do the following it says that the matrix dimension don't match to extract the beta coefficients with 3dmaskdump:
3dmaskdump -o V3A_V3BDumpMask_7T_v3_surf.txt -noijk -mask 7T_V3A_V3B_mask.nii.niml.dset 'stats.Subject_109123_7T+tlrc.BRIK[1]'
how do I fix this issue to be able to extract the beta coefficients with the corresponding ROI regions from the surface?
You still need to convert the surface dataset to a volumetric dataset, to be able to use it with a volumetric dataset. Converting the ROI->surface is a good first step, but then you would want to use 3dSurf2Vol to convert that to a volume. This is described in this AFNI Academy video about using SUMA (from about that time in the link and onwards.
After that, you should be able to use the volumetric ROI as a mask for picking out voxels from the volumetric dset.
On a very minor side note, I tend to stay away from using *.BRIK files in scripts with command names; this is because they could be zipped (*.BRIK.gz) or unzipped depending on the system settings or choices later, so that a script might appear broken later even though the data actually exists. I think it is better to use *.HEAD files, since those are typically never zipped (or of course *.nii or *.nii.gz work in scripts, as well).
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