Because we have seen some of the issues Bob mentioned specifically in the OpenFMRI dataset, I took a quick look at the linked data. If I use 3dinfo on this (see below), the voxels are 3x3x3.5mm, somewhat typical for fMRI; I don't see the 1x1x1mm data you have, so something else happened to your data. There are a few more problems to look out for on this data, however. You will notice the BOLD datasets are acquired with two different orientations, RAI or RPI. I think the same orientation is used within subject for both BOLD runs, but this could lead to problems at the group level analysis if you assume the same grid, so you will have to be careful about that. In the BOLD data, the qform_code and sform_code values are set to 1 and 2, respectively. AFNI, by default, treats these as "tlrc" view, assuming these have been registered to a standard space. That makes it a bit tricky to view the BOLD data over the anatomical data. Set the AFNI environment variable, AFNI_NIFTI_VIEW, to orig in the shell or in your .afnirc file.

The anatomical data is slightly oblique at 3.5 degrees, but our standard processing should handle that. Additionally, the anatomical data varies in its resolution across subjects. Most, but not all subjects, have voxel sizes around 1.2mm. Orientations of those datasets are again surprisingly varied though with orientation orders of RPI and ASR. I'm not sure if that will affect your processing, but something else to keep in mind as you go.

openfmri/ds000109_R2.0.2] glend% 3dinfo -prefix -orient -d3 -o3 sub*/func/*.nii.gz
** AFNI converts NIFTI_datatype=512 (UINT16) in file sub-01/func/sub-01_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
sub-01_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz RAI 3.000000 3.000000 3.539701 -113.395279 -136.387894 -35.929810
sub-01_task-theoryofmindwithmanualresponse_run-02_bold.nii.gz RAI 3.000000 3.000000 3.539701 -113.786499 -136.681213 -34.904900
sub-02_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz RAI 3.000000 3.000000 3.539928 -86.994926 -165.123245 -36.951183
sub-02_task-theoryofmindwithmanualresponse_run-02_bold.nii.gz RAI 3.000000 3.000000 3.539928 -87.875198 -163.503479 -41.624382
sub-03_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz RPI 3.000000 -3.000000 3.539913 -110.812683 66.151535 -40.571239
sub-03_task-theoryofmindwithmanualresponse_run-02_bold.nii.gz RPI 3.000000 -3.000000 3.539913 -110.701958 66.595985 -40.198555
sub-05_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz RPI 3.000000 -3.000000 3.539997 -103.874046 64.358917 -71.371323
sub-05_task-theoryofmindwithmanualresponse_run-02_bold.nii.gz RPI 3.000000 -3.000000 3.539997 -100.284164 66.343353 -64.523521
sub-07_task-theoryofmindwithmanualresponse_run-01_bold.nii.gz RPI 3.000000 -3.000000 3.540012 -121.250893 47.643005 -61.460804
sub-07_task-theoryofmindwithmanualresponse_run-02_bold.nii.gz RPI 3.000000 -3.000000 3.540012 -121.338051 48.233105 -61.566978