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

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_dualecho_noslicetiming_ver01

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_general_noreslice_ver00

aap_spmanalysis_autotr_noreslice_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_general_ver02

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_general_withmodel_ver02

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_general_withundistort_ver02

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_noslicetiming_withmodel_ver00

aap_spmanalysis_autotr_noreslice_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_notfmri_ver01

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_realignunwarp_ver00

aap_spmanalysis_autotr_resliceall_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_slicetimingfirst_withmodel_ver00

aap_spmanalysis_autotr_noreslice_ver00

aap_acq_details_ver00

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]

aap_directory_conventions_ver00

aap_options_ver00

aap_tasklist_structuralsonly

aap_spmanalysis_autotr_noreslice_ver00

aap_acq_details_ver00

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]