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| ''' Contents ''' [[TableOfContents]] | ''' Contents ''' <<TableOfContents>> |
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| = Recipes that are available = These apply to the development version, soon to be released (Sep 2006). This first section describes available recipes. The next section discusses issues that might help you choose the appropriate one for you. |
= 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] || |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || || aamod_tsdiffana || Run tsdiffana || f || || aamod_realign || SPM5 realignment || f || || aamod_slicetiming || SPM5 slice timing || rf || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || arf || || aamod_norm_noss || SPM5 normalisation/segment || arf || || aamod_norm_write || SPM5 write normalised || arf || || aamod_smooth || SPM5 smooth || warf || |
|| ''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] || |
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| Slice timing first, with model |
Default recipe with model |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || || aamod_tsdiffana || Run tsdiffana || f || || aamod_realign || SPM5 realignment || f || || aamod_slicetiming || SPM5 slice timing || rf || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || arf || || aamod_norm_noss || SPM5 normalisation/segment || arf || || aamod_norm_write || SPM5 write normalised || arf || || aamod_smooth || SPM5 smooth || warf || || aamod_firstlevel_model || SPM5 first level model || swarf || || aamod_firstlevel_contrasts || SPM5 contrasts || swarf || || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
|| ''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] || |
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| Recipe without slice timing. Suitable for sparse imaging, or when you are going to but event derivatives in your model. |
Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || || aamod_tsdiffana || Run tsdiffana || f || || aamod_realign || SPM5 realignment || f || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || f || || aamod_norm_noss || SPM5 normalisation/segment || f || || aamod_norm_write || SPM5 write normalised || f || || aamod_smooth || SPM5 smooth || wf || || aamod_firstlevel_model || SPM5 first level model || swf || || aamod_firstlevel_contrasts || SPM5 contrasts || swf || || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
|| ''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] || |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || || aamod_tsdiffana || Run tsdiffana || f || || aamod_realignunwarp || SPM5 realign and unwarp || f || || aamod_slicetiming || SPM5 slice timing || uf || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || auf || || aamod_norm_noss || SPM5 normalisation/segment || auf || || aamod_norm_write || SPM5 write normalised || auf || || aamod_smooth || SPM5 smooth || wauf || |
|| ''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] || |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || || aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || || aamod_tsdiffana || Run tsdiffana || f || || aamod_slicetiming || SPM5 slice timing || f || || aamod_realign || SPM5 realignment || af || || aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || af || || aamod_norm_noss || SPM5 normalisation/segment || af || || aamod_norm_write || SPM5 write normalised || af || || aamod_smooth || SPM5 smooth || waf || || aamod_firstlevel_model || SPM5 first level model || swaf || || aamod_firstlevel_contrasts || SPM5 contrasts || swaf || || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
|| ''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] || |
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| || ''stage'' || ''description'' || ''EPI prefix for input'' || || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || || aamod_copystructural || Structural dicom to nifti and copying || || = 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 [wiki: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. |
|| ''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] || |
This manual is for aa parallel version 2.2 and earlier. You might prefer the new aa wiki for aa version 3.0 and above or information on cloud execution
Contents
Contents
- Considerations when choosing a recipe
-
Recipes that are available in aa version 2 devel (launch with aa_ver2_devel)
- aarecipe_dualecho_noslicetiming_ver01.m
- aarecipe_general_noreslice_ver00.m
- aarecipe_general_ver02.m
- aarecipe_general_withmodel_ver01.m
- aarecipe_general_withundistort_ver02.m
- aarecipe_noslicetiming_withmodel_ver00.m
- aarecipe_notfmri_ver01.m
- aarecipe_realignunwarp_nomodel_ver00.m
- aarecipe_slicetimingfirst_withmodel_ver00.m
- aarecipe_structuralsonly_ver00.m
-
Recipes that are available in aa version 2.0 (launch with aa_ver20)
- aarecipe_dualecho_noslicetiming_ver01.m
- aarecipe_general_noreslice_ver00.m
- aarecipe_general_ver02.m
- aarecipe_general_withmodel_ver01.m
- aarecipe_general_withundistort_ver02.m
- aarecipe_noslicetiming_withmodel_ver00.m
- aarecipe_notfmri_ver01.m
- aarecipe_realignunwarp_nomodel_ver00.m
- aarecipe_slicetimingfirst_withmodel_ver00.m
- aarecipe_structuralsonly_ver00.m
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 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] |