diff --git a/preprocessing_rsfmri/model_specification.m b/preprocessing_rsfmri/model_specification.m new file mode 100644 index 0000000000000000000000000000000000000000..cc0a9bc5064e8093f34a1eec420e9801f1025b45 --- /dev/null +++ b/preprocessing_rsfmri/model_specification.m @@ -0,0 +1,61 @@ + + +tr = 0.955; +n_slices = 60; +subdirectory = [subdir, '/', subname]; +fmap_file = [subdirectory, '/fmap/', subname, '_acq-topup2_fieldmap.nii,1']; +mag_fmap_file = [subdirectory, '/fmap/', subname, '_acq-topup2_magnitude.nii,1']; +epi_ref = [subdirectory, '/func/a', subname, '_task-rest_bold.nii,1']; + +T1_ref = [subdirectory, '/anat/masked_msanlm_', subname, '_T1w.nii,1']; + + +bold_img = [subdirectory, '/func/', subname, '_task-rest_bold.nii']; +realigned_bold = [subdirectory, '/func/ua', subname, '_task-rest_bold.nii']; +coreg_ref=[subdirectory, '/func/localizer/vol/u', subname, '_task-localizer_bold.nii,1']; + +c2_img = [subdirectory, '/anat/c2sanlm_', subname, '_T1w.nii,1']; +c3_img = [subdirectory, '/anat/c3sanlm_', subname, '_T1w.nii,1']; + +rp_file = [subdirectory, '/func/rest/rp_a', subname, '_task-rest_bold.txt']; + + + +n_comp = 12; + +% % ------------------------------------------------------------------------ +job_id = 1; +% % + + +%% Model Specification (GLM) +%% Make Directory +f_parent=[subdirectory,'/glm']; +matlabbatch{job_id}.cfg_basicio.file_dir.dir_ops.cfg_mkdir.parent = {f_parent}; +matlabbatch{job_id}.cfg_basicio.file_dir.dir_ops.cfg_mkdir.name = 'noisefiltering'; +job_id = job_id + 1; +%% Model Specification: GLM +spec_dir=[subdirectory ,'/glm/noisefiltering']; +scan=[subdirectory, '/func/ua', subname ,'_task-rest_bold.nii']; +reg=[subdirectory ,'/func/', subname ,'_task-rest_noise.txt']; +fmask=[subdirectory, '/func/ua', subname ,'_task-rest_bold_fullimage_mask.nii']; +matlabbatch{job_id}.spm.stats.fmri_spec.dir = {spec_dir}; +matlabbatch{job_id}.spm.stats.fmri_spec.timing.units = 'secs'; +matlabbatch{job_id}.spm.stats.fmri_spec.timing.RT = 0.955; +matlabbatch{job_id}.spm.stats.fmri_spec.timing.fmri_t = 12; +matlabbatch{job_id}.spm.stats.fmri_spec.timing.fmri_t0 = 6; +matlabbatch{job_id}.spm.stats.fmri_spec.sess.scans = {scan}; +matlabbatch{job_id}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {}); +matlabbatch{job_id}.spm.stats.fmri_spec.sess.multi = {''}; +matlabbatch{job_id}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {}); +matlabbatch{job_id}.spm.stats.fmri_spec.sess.multi_reg = {reg}; +matlabbatch{job_id}.spm.stats.fmri_spec.sess.hpf = 128; +matlabbatch{job_id}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {}); +matlabbatch{job_id}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0]; +matlabbatch{job_id}.spm.stats.fmri_spec.volt = 1; +matlabbatch{job_id}.spm.stats.fmri_spec.global = 'None'; +matlabbatch{job_id}.spm.stats.fmri_spec.mthresh = 0; +matlabbatch{job_id}.spm.stats.fmri_spec.mask = {fmask}; +matlabbatch{job_id}.spm.stats.fmri_spec.cvi = 'AR(1)'; +job_id = job_id + 1; +