Dear SPM gurus,
I have been tasked to figure out why we're seeing what appears to be a checkerboard banding pattern in our mwc1 output images. I know it's common practice to smooth these images before analysis (we use an 8x8x8mm smoothing kernel), but we were wondering if this is something commonly seen. For a few datasets (ADNI, ADNI-DOD) this is not very pronounced, but in other datasets (src: BLSA, clinical trials) it is quite pronounced. It doesn't seem to be dependent on the original byte depth of the image.
I seem to be unable to attach or embed a graphic (would be much easier, 1000 words, etc), but the pattern is very regular (basically higher intensity squares in axial and coronal views, with the sagittal banding often at an angle.
Could this be a result of upsampling? TPM.nii is 1.5mm^3 and our images are routinely 1x1x1 or 1x1x1.2mm^3
Some other reason?
Thanks in advance for any replies/insight on this matter.
Sincerely,
Randy
PS. We're using the exact same parameter settings in SPM > Segment (SPM12) for all the sets.
%-----------------------------------------------------------------------
% Job saved on 29-Nov-2022 09:57:37 by cfg_util (rev $Rev: 6942 $)
% spm SPM - SPM12 (7219)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.spatial.preproc.channel.vols = {'C:\Users\Randolph\Desktop\WBI_2nd-look_SegWarp_S_0864_112922\2nd-look_SegWarp_S_0864_wbi-T1-mgz_112922\WBI-WCM__S_0864__MRI__BL__20210119__T1-mgz.nii,1'};
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {'C:\spm\spm12\tpm\TPM.nii,1'};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'C:\spm\spm12\tpm\TPM.nii,2'};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'C:\spm\spm12\tpm\TPM.nii,3'};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'C:\spm\spm12\tpm\TPM.nii,4'};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'C:\spm\spm12\tpm\TPM.nii,5'};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'C:\spm\spm12\tpm\TPM.nii,6'};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [1 1];
matlabbatch{2}.spm.spatial.preproc.channel.vols = {'C:\Users\Randolph\Desktop\WBI_2nd-look_SegWarp_S_0864_112922\2nd-look_SegWarp_S_0864_wbi_112922\WBI-WCM__S_0864__MRI__BL__20210119.nii,1'};
matlabbatch{2}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{2}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{2}.spm.spatial.preproc.channel.write = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(1).tpm = {'C:\spm\spm12\tpm\TPM.nii,1'};
matlabbatch{2}.spm.spatial.preproc.tissue(1).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(1).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(1).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(2).tpm = {'C:\spm\spm12\tpm\TPM.nii,2'};
matlabbatch{2}.spm.spatial.preproc.tissue(2).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(2).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(2).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(3).tpm = {'C:\spm\spm12\tpm\TPM.nii,3'};
matlabbatch{2}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(3).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(3).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(4).tpm = {'C:\spm\spm12\tpm\TPM.nii,4'};
matlabbatch{2}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{2}.spm.spatial.preproc.tissue(4).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(4).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(5).tpm = {'C:\spm\spm12\tpm\TPM.nii,5'};
matlabbatch{2}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{2}.spm.spatial.preproc.tissue(5).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(5).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(6).tpm = {'C:\spm\spm12\tpm\TPM.nii,6'};
matlabbatch{2}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(6).native = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(6).warped = [1 1];
matlabbatch{2}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{2}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{2}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{2}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{2}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{2}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{2}.spm.spatial.preproc.warp.write = [1 1];
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