I note your implementation of DARTEL sometimes creates tears in the image when they are created. This looks like black dots or streaks when viewing the images. I think this is because you are setting the FWHM to zero, while John Ashburner suggests "normalise to MNI space option is intended to be used with smoothing". This issue has been described previously here
http://rfmri.org/content/problem-normalization
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&P=R74748&1=spm&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
I would suggest that the user's desired FWHM smoothing is applied during the DARTEL reslicing. Therefore, smoothing will not be done as a separate stage, but rather when in the following places in your code:
Subfunctions/y_Normalize_WriteToMNI_DARTEL.m
SPMJOB.matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0];
DPARSFA_run.m
788
matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0]; % Do not want to perform
2282
SPMJOB.matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0];
I note your implementation of DARTEL sometimes creates tears in the image when they are created. This looks like black dots or streaks when viewing the images. I think this is because you are setting the FWHM to zero, while John Ashburner suggests "normalise to MNI space option is intended to be used with smoothing". This issue has been described previously here
http://rfmri.org/content/problem-normalization
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&P=R74748&1=spm&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
I would suggest that the user's desired FWHM smoothing is applied during the DARTEL reslicing. Therefore, smoothing will not be done as a separate stage, but rather when in the following places in your code:
Subfunctions/y_Normalize_WriteToMNI_DARTEL.m
SPMJOB.matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0];
DPARSFA_run.m
788
matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0]; % Do not want to perform
2282
SPMJOB.matlabbatch{1,1}.spm.tools.dartel.mni_norm.fwhm=[0 0 0];