Update PreCompMotionCorrection.m

functions/PreCompMotionCorrection.m

@@ -8,37 +8,41 @@
 for idx = 1:numel(BIDS.subjects)
     subj = BIDS.subjects(idx).name;
     ses = BIDS.subjects(idx).session;
+
+    if ~isempty(BIDS.subjects(idx).pet)
     file = fullfile(BIDS.subjects(idx).path, 'pet', BIDS.subjects(idx).pet(1).filename);
 
     output_name = fullfile(output_dir, subj, ses, ...
         'pet', [subj '_' ses '_desc-mc_pet.nii.gz']);
 
+    output_json = fullfile(output_dir, subj, ses, ...
+        'pet', [subj '_' ses '_desc-mc_pet.json']);
+
     output_confounds = fullfile(output_dir, subj, ses, ...
         'pet', [subj '_' ses '_desc-confounds_timeseries.tsv']);
 
-    mc_dir = dir([BIDS.pth '/derivatives/hmc_workflow/*' erase(ses,'ses-') '*' strrep(BIDS.subjects(idx).name(end-2:end),'-','_') ]);
-    mc_file = fullfile(mc_dir.folder, mc_dir.name, 'concat_frames/mc.nii.gz');
-    movement = fullfile(mc_dir.folder, mc_dir.name, 'plot_motion/movement.png');
-    rotation = fullfile(mc_dir.folder, mc_dir.name, 'plot_motion/rotation.png');
-    translation = fullfile(mc_dir.folder, mc_dir.name, 'plot_motion/translation.png');
-    confounds = fullfile(mc_dir.folder, mc_dir.name, 'hmc_movement_output/hmc_confounds.tsv');
-
+
+    mc_file = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_desc-mc_pet.nii.gz']);
+    mc_json = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_desc-mc_pet.json']);
+    movement = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_movement.png']);
+    rotation = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_rotation.png']);
+    translation = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_translation.png']);
+    confounds = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_desc-confounds_timeseries.tsv']);
+    nmc_plot = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_desc-without_motion_correction.gif']);
+    mc_plot = fullfile([BIDS.pth '/derivatives/petprep_hmc/' subj '/' ses '/' subj '_' ses '_desc-with_motion_correction.gif']);
+
+    if exist(mc_file,"file")
     mkdir(fullfile(output_dir, 'logs', subj))
     copyfile(mc_file, output_name);
+    copyfile(mc_json, output_json);
     copyfile(confounds, output_confounds);
     copyfile(movement, fullfile(output_dir, 'logs', subj, [subj '_' ses '_movement.png']))
     copyfile(rotation, fullfile(output_dir, 'logs', subj, [subj '_' ses '_rotation.png']))
     copyfile(translation, fullfile(output_dir, 'logs', subj, [subj '_' ses '_translation.png']))
+    copyfile(nmc_plot, fullfile(output_dir, 'logs', subj, [subj '_' ses '_desc-without_motion_correction.gif']))
+    copyfile(mc_plot, fullfile(output_dir, 'logs', subj, [subj '_' ses '_desc-with_motion_correction.gif']))
 
-    mc = struct;
-    mc.Description = 'Motion-corrected PET file';
-    mc.Sources = erase(file,pwd);
-    mc.ReferenceImage = 'Robust template using mri_robust_register';
-    mc.CostFunction = 'ROB';
-    mc.QC = '';
-    mc.SoftwareName = 'PETPrep HMC workflow';
-    mc.SoftwareVersion = 'v. 0.0.1';
-    bids.util.jsonwrite(fullfile(output_dir, subj, ses, ...
-        'pet', [subj '_' ses '_desc-mc_pet.json']),mc);
+    end
+    end
 end