diff --git a/narps_open/pipelines/matlabbatch_R5K7.m b/narps_open/pipelines/matlabbatch_R5K7.m index ed2b3f98..7e90190a 100644 --- a/narps_open/pipelines/matlabbatch_R5K7.m +++ b/narps_open/pipelines/matlabbatch_R5K7.m @@ -81,6 +81,14 @@ % calculated transformation between anat and standardized space % Coreg each sbref onto mean unwarp + +% --> For each run, the distortion-corrected single-band reference EPI image +% was co-registered to the mean EPI image obtained from Realignment & Unwarping + % using normalised mutual information. + +% Note in Python implem: This sounds like there were 4 coreg and not a single +% as done below (4 coregs were implemented in the Python code) + matlabbatch{end+1}.spm.spatial.coreg.estimate.ref(1) = { 'ABS_PATH/unwarped_mean_image.nii' }; @@ -113,6 +121,9 @@ % keeps the same name as before *but* the header has been modified to apply % the coregistration' + +% Note in Python implem: The coreg are done separatly in each run and therefore +% other only includes 'usub-001_task-MGT_run-01_bold.nii' matlabbatch{end+1}.spm.spatial.coreg.estimate.ref(1) = { 'ABS_PATH/c1sub-001_T1w.nii' }; @@ -286,6 +297,22 @@ with open(event_file, 'rt') as file: I think this means we have a single stat model with the 4 factors and the 2 groups and that the contrast. +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(1).name = 'Factor'; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(1).dept = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(1).variance = 1; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(1).gmsca = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(1).ancova = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(2).name = 'Group'; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(2).dept = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(2).variance = 1; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(2).gmsca = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fac(2).ancova = 0; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fsuball.fsubject.scans = ''; +matlabbatch{1}.spm.stats.factorial_design.des.fblock.fsuball.fsubject.conds = [1 1 + 2 1 + 3 1 + 4 1]; + % ##### 6) Group-level contrast % --> inference_contrast_effect : Linear T contrasts for the two parameters of