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 ''' Contents ''' [[TableOfContents]]

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= Recipes that are available =
These apply to the development version, soon to be released (Sep 2006).


= 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.

== 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'' ||
|| 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 ||
== aarecipe_general_withmodel_ver01.m ==
Slice timing first, 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'' ||
|| 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 || ||
== aarecipe_noslicetiming_withmodel_ver00.m ==
Recipe without slice timing. Suitable for sparse imaging, or when you are going to but event 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'' ||
|| 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 || ||
== 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'' ||
|| 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 ||
== 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'' ||
|| 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 || ||
== 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'' ||
|| 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 ||  ||