AutomaticAnalysisRecipes - MRC CBU Imaging Wiki

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location: AutomaticAnalysisRecipes

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]