## page was renamed from AutomaticAnalysis <> ---- ''' Contents ''' <> ---- = Considerations when choosing a recipe = == Slice timing or not? == See the page on SliceTiming for a discussion == Realign and unwarp or just realign? == See the [[MotionCorrection#realign_unwarp|Realign Unwarp]] section of the MotionCorrection page. == Scripting your modelling? == The newer releases of aa allow scripted first level modelling, first level contrasts, and second level modelling. The first level modelling requires you to do a little coding, to specify your design. Unless you are the one neuroimager on the planet that gets the design of the analysis of their experiment exactly right first time, I would recommend this - you'll find it a little effort now for a big gain later. = Recipes that are available in aa version 2 devel (launch with aa_ver2_devel) = || aarecipe_dualecho_noslicetiming_ver01.m || For dual echo (GE/SE) with undistortion but no slice timing || || aarecipe_general_noreslice_ver00.m || Default recipe without model || || aarecipe_general_ver02.m || Default recipe without model || || aarecipe_general_withmodel_ver01.m || Default recipe with model || || aarecipe_general_withundistort_ver02.m || Default recipe without model || || aarecipe_noslicetiming_withmodel_ver00.m || Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. || || aarecipe_notfmri_ver01.m || Converts structurals & special series as specified in 5th parameter of aas_addsubject command || || aarecipe_realignunwarp_nomodel_ver00.m || Recipe using realign & unwarp without model || || aarecipe_slicetimingfirst_withmodel_ver00.m || Slice timing first, with model || || aarecipe_structuralsonly_ver00.m || Recipe that only processes structurals || == aarecipe_dualecho_noslicetiming_ver01.m == For dual echo (GE/SE) with undistortion but no slice timing === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_dualecho_noslicetiming_ver01 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || aamod_convert_epis || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_convertfieldmaps || Convert fieldmaps || || aamod_newsubj_init || || aamod_fieldmap_undistort || Fieldmap undistort v4 || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || u || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || ur || [previous] || || aamod_norm_write || SPM5 write normalised || ur || [previous] || || aamod_smooth || SPM5 smooth || wur || [previous] || == aarecipe_general_noreslice_ver00.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_noreslice_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || aamod_realign || || aamod_norm_noss || SPM5 normalisation/segment || a || [previous] || || aamod_norm_write || SPM5 write normalised || a || [previous] || || aamod_smooth || SPM5 smooth || wa || [previous] || == aarecipe_general_ver02.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || aamod_realign || || aamod_norm_noss || SPM5 normalisation/segment || ar || [previous] || || aamod_norm_write || SPM5 write normalised || ar || [previous] || || aamod_smooth || SPM5 smooth || war || [previous] || == aarecipe_general_withmodel_ver01.m == Default recipe with model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_withmodel_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || aamod_realign || || aamod_norm_noss || SPM5 normalisation/segment || ar || [previous] || || aamod_norm_write || SPM5 write normalised || ar || [previous] || || aamod_smooth || SPM5 smooth || war || [previous] || || aamod_firstlevel_model || SPM5 first level model || swar || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || swar || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_general_withundistort_ver02.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_withundistort_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_convertfieldmaps || Convert fieldmaps || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || [previous] || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || [previous] || || aamod_fieldmap_undistort || Fieldmap undistort v4 || r || [previous] || || aamod_slicetiming || SPM5 slice timing || ur || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || u || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || aur || [previous] || || aamod_norm_write || SPM5 write normalised || aur || [previous] || || aamod_smooth || SPM5 smooth || waur || [previous] || == aarecipe_noslicetiming_withmodel_ver00.m == Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_noslicetiming_withmodel_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || [previous] || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || || [previous] || || aamod_norm_write || SPM5 write normalised || || [previous] || || aamod_smooth || SPM5 smooth || w || [previous] || || aamod_firstlevel_model || SPM5 first level model || sw || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || sw || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_notfmri_ver01.m == Converts structurals & special series as specified in 5th parameter of aas_addsubject command === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_notfmri_ver01 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convertspecialseries || Convert special series || || [previous] || == aarecipe_realignunwarp_nomodel_ver00.m == Recipe using realign & unwarp without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_realignunwarp_ver00 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realignunwarp || SPM5 realign and unwarp || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || u || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || u || || || aamod_norm_noss || SPM5 normalisation/segment || au || [previous] || || aamod_norm_write || SPM5 write normalised || au || [previous] || || aamod_smooth || SPM5 smooth || wau || [previous] || == aarecipe_slicetimingfirst_withmodel_ver00.m == Slice timing first, with model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_slicetimingfirst_withmodel_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_slicetiming || SPM5 slice timing || || aamod_convert_epis || || aamod_realign || SPM5 realignment || a || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || a || [previous] || || aamod_norm_write || SPM5 write normalised || a || [previous] || || aamod_smooth || SPM5 smooth || wa || [previous] || || aamod_firstlevel_model || SPM5 first level model || swa || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || swa || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_structuralsonly_ver00.m == Recipe that only processes structurals === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_structuralsonly || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || = Recipes that are available in aa version 2.0 (launch with aa_ver20) = || aarecipe_dualecho_noslicetiming_ver01.m || For dual echo (GE/SE) with undistortion but no slice timing || || aarecipe_general_noreslice_ver00.m || Default recipe without model || || aarecipe_general_ver02.m || Default recipe without model || || aarecipe_general_withmodel_ver01.m || Default recipe with model || || aarecipe_general_withundistort_ver02.m || Default recipe without model || || aarecipe_noslicetiming_withmodel_ver00.m || Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. || || aarecipe_notfmri_ver01.m || Converts structurals & special series as specified in 5th parameter of aas_addsubject command || || aarecipe_realignunwarp_nomodel_ver00.m || Recipe using realign & unwarp without model || || aarecipe_slicetimingfirst_withmodel_ver00.m || Slice timing first, with model || || aarecipe_structuralsonly_ver00.m || Recipe that only processes structurals || == aarecipe_dualecho_noslicetiming_ver01.m == For dual echo (GE/SE) with undistortion but no slice timing === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_dualecho_noslicetiming_ver01 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || aamod_convert_epis || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_convertfieldmaps || Convert fieldmaps || || aamod_newsubj_init || || aamod_fieldmap_undistort || Fieldmap undistort v4 || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || ur || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || ur || [previous] || || aamod_norm_write || SPM5 write normalised || ur || [previous] || || aamod_smooth || SPM5 smooth || wur || [previous] || == aarecipe_general_noreslice_ver00.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_noreslice_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || aamod_realign || || aamod_norm_noss || SPM5 normalisation/segment || a || [previous] || || aamod_norm_write || SPM5 write normalised || a || [previous] || || aamod_smooth || SPM5 smooth || wa || [previous] || == aarecipe_general_ver02.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || r || aamod_realign || || aamod_norm_noss || SPM5 normalisation/segment || ar || [previous] || || aamod_norm_write || SPM5 write normalised || ar || [previous] || || aamod_smooth || SPM5 smooth || war || [previous] || == aarecipe_general_withmodel_ver01.m == Default recipe with model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_withmodel_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || r || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || r || || || aamod_norm_noss || SPM5 normalisation/segment || ar || [previous] || || aamod_norm_write || SPM5 write normalised || ar || [previous] || || aamod_smooth || SPM5 smooth || war || [previous] || || aamod_firstlevel_model || SPM5 first level model || swar || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || swar || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_general_withundistort_ver02.m == Default recipe without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_general_withundistort_ver02 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_convertfieldmaps || Convert fieldmaps || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || [previous] || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || [previous] || || aamod_fieldmap_undistort || Fieldmap undistort v4 || r || [previous] || || aamod_slicetiming || SPM5 slice timing || ur || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || aur || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || aur || [previous] || || aamod_norm_write || SPM5 write normalised || aur || [previous] || || aamod_smooth || SPM5 smooth || waur || [previous] || == aarecipe_noslicetiming_withmodel_ver00.m == Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_noslicetiming_withmodel_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || [previous] || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realign || SPM5 realignment || || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || || [previous] || || aamod_norm_write || SPM5 write normalised || || [previous] || || aamod_smooth || SPM5 smooth || w || [previous] || || aamod_firstlevel_model || SPM5 first level model || sw || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || sw || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_notfmri_ver01.m == Converts structurals & special series as specified in 5th parameter of aas_addsubject command === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_notfmri_ver01 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] || || aamod_convertspecialseries || Convert special series || || [previous] || == aarecipe_realignunwarp_nomodel_ver00.m == Recipe using realign & unwarp without model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_realignunwarp_ver00 || || aap_spmanalysis_autotr_resliceall_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_realignunwarp || SPM5 realign and unwarp || || aamod_convert_epis || || aamod_slicetiming || SPM5 slice timing || u || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || u || || || aamod_norm_noss || SPM5 normalisation/segment || au || [previous] || || aamod_norm_write || SPM5 write normalised || au || [previous] || || aamod_smooth || SPM5 smooth || wau || [previous] || == aarecipe_slicetimingfirst_withmodel_ver00.m == Slice timing first, with model === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_slicetimingfirst_withmodel_ver00 || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || aamod_newsubj_init || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || aamod_newsubj_init || || aamod_tsdiffana || Run tsdiffana || || [previous] || || aamod_slicetiming || SPM5 slice timing || || aamod_convert_epis || || aamod_realign || SPM5 realignment || a || [previous] || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || a || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || a || [previous] || || aamod_norm_write || SPM5 write normalised || a || [previous] || || aamod_smooth || SPM5 smooth || wa || [previous] || || aamod_firstlevel_model || SPM5 first level model || swa || [previous] || || aamod_firstlevel_contrasts || SPM5 contrasts || swa || [previous] || || aamod_secondlevel_model || SPM5 second level (RFX) model || || [previous] || == aarecipe_structuralsonly_ver00.m == Recipe that only processes structurals === Parameter sets === || aap_directory_conventions_ver00 || || aap_options_ver00 || || aap_tasklist_structuralsonly || || aap_spmanalysis_autotr_noreslice_ver00 || || aap_acq_details_ver00 || === Tasklist === || ''stage'' || ''description'' || ''EPI prefix for input'' || ''To be completed first''|| || aamod_study_init || Initialise study || || [previous] || || aamod_newsubj_init || Make subject directory || || [previous] || || aamod_converttmaps || Convert real time t statistic outputs || || [previous] || || aamod_copystructural || Structural dicom to nifti and copying || || [previous] ||