AutomaticAnalysisRecipes - MRC CBU Imaging Wiki

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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.

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

attachment:test.jpg

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.