Diff for "AutomaticAnalysisRecipes" - MRC CBU Imaging Wiki
location: Diff for "AutomaticAnalysisRecipes"
Differences between revisions 48 and 49
Revision 48 as of 2007-02-15 09:53:28
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Editor: RhodriCusack
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Revision 49 as of 2007-08-31 15:47:14
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Editor: RhodriCusack
Comment:
Deletions are marked like this. Additions are marked like this.
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These apply to the development version (aa_ver1_devel), soon to be released.
These apply to 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 ||
Line 29: Line 31:
|| aarecipe_general_withundistort_ver02.m || Default recipe with undistort and model || || aarecipe_general_withundistort_ver02.m || Default recipe without model ||
Line 35: Line 37:
== 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'' ||
|| aamod_study_init || Initialise study || || ||
|| aamod_newsubj_init || Make subject directory || || ||
|| aamod_converttmaps || Convert real time t statistic outputs || || ||
|| aamod_convert_epis || Performing dicom to nifti conversion of EPIs || || ||
|| aamod_copystructural || Structural dicom to nifti and copying || || ||
|| aamod_tsdiffana || Run tsdiffana || || ||
|| aamod_realign || SPM5 realignment || || ||
|| aamod_convertfieldmaps || Convert fieldmaps || || ||
|| aamod_fieldmap_undistort || Fieldmap undistort v4 || r || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || ur || ||
|| aamod_norm_noss || SPM5 normalisation/segment || ur || ||
|| aamod_norm_write || SPM5 write normalised || ur || ||
|| aamod_smooth || SPM5 smooth || wur || ||
== 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'' ||
|| 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 || || ||
|| aamod_realign || SPM5 realignment || || ||
|| aamod_slicetiming || SPM5 slice timing || || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || a || ||
|| aamod_norm_noss || SPM5 normalisation/segment || a || ||
|| aamod_norm_write || SPM5 write normalised || a || ||
|| aamod_smooth || SPM5 smooth || wa || ||
Line 45: Line 92:
|| 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_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 ||  || ||
|| aamod_realign || SPM5 realignment ||  || ||
|| aamod_slicetiming || SPM5 slice timing || r || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || r || ||
|| aamod_norm_noss || SPM5 normalisation/segment || ar || ||
|| aamod_norm_write || SPM5 write normalised || ar || ||
|| aamod_smooth || SPM5 smooth || war || ||
Line 67: Line 114:
|| 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 || ||
|| 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 ||  || ||
|| aamod_realign || SPM5 realignment ||  || ||
|| aamod_slicetiming || SPM5 slice timing || r || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || ar || ||
|| aamod_norm_noss || SPM5 normalisation/segment || ar || ||
|| aamod_norm_write || SPM5 write normalised || ar || ||
|| aamod_smooth || SPM5 smooth || war || ||
|| aamod_firstlevel_model || SPM5 first level model || swar || ||
|| aamod_firstlevel_contrasts || SPM5 contrasts || swar || ||
|| aamod_secondlevel_model || SPM5 second level (RFX) model || ||  ||
Line 83: Line 130:
Default recipe with undistort and model Default recipe without model
Line 92: Line 139:
|| aamod_study_init || Initialise study || ||
|| aamod_newsubj_init || Make subject directory || ||
|| aamod_converttmaps || Convert real time t statistic outputs || ||
|| aamod_convertfieldmaps || Convert fieldmaps || ||
|| 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_fieldmap_undistort || Fieldmap undistort v4 || rf ||
|| aamod_slicetiming || SPM5 slice timing || urf ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || aurf ||
|| aamod_norm_noss || SPM5 normalisation/segment || aurf ||
|| aamod_norm_write || SPM5 write normalised || aurf ||
|| aamod_smooth || SPM5 smooth || waurf ||
|| aamod_firstlevel_model || SPM5 first level model || swaurf ||
|| aamod_firstlevel_contrasts || SPM5 contrasts || swaurf ||
|| aamod_secondlevel_model || SPM5 second level (RFX) model || ||
|| aamod_study_init || Initialise study || || ||
|| aamod_newsubj_init || Make subject directory || ||  ||
|| aamod_converttmaps || Convert real time t statistic outputs || ||  ||
|| aamod_convertfieldmaps || Convert fieldmaps || ||  ||
|| aamod_copystructural || Structural dicom to nifti and copying || || ||
|| aamod_convert_epis || Performing dicom to nifti conversion of EPIs || ||  ||
|| aamod_tsdiffana || Run tsdiffana ||  || ||
|| aamod_realign || SPM5 realignment ||  || ||
|| aamod_fieldmap_undistort || Fieldmap undistort v4 || r || ||
|| aamod_slicetiming || SPM5 slice timing || ur || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || aur || ||
|| aamod_norm_noss || SPM5 normalisation/segment || aur || ||
|| aamod_norm_write || SPM5 write normalised || aur || ||
|| aamod_smooth || SPM5 smooth || waur || ||
Line 119: Line 163:
|| 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 || ||
|| 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 ||  || ||
|| aamod_realign || SPM5 realignment ||  || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping ||  || ||
|| aamod_norm_noss || SPM5 normalisation/segment ||  || ||
|| aamod_norm_write || SPM5 write normalised ||  || ||
|| aamod_smooth || SPM5 smooth || w || ||
|| aamod_firstlevel_model || SPM5 first level model || sw || ||
|| aamod_firstlevel_contrasts || SPM5 contrasts || sw || ||
|| aamod_secondlevel_model || SPM5 second level (RFX) model || ||  ||
Line 143: Line 187:
|| 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_convertspecialseries || Convert special series || ||
|| 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_convertspecialseries || Convert special series || ||  ||
Line 158: Line 202:
|| 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 ||
|| 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 ||  || ||
|| aamod_realignunwarp || SPM5 realign and unwarp ||  || ||
|| aamod_slicetiming || SPM5 slice timing || u || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || au || ||
|| aamod_norm_noss || SPM5 normalisation/segment || au || ||
|| aamod_norm_write || SPM5 write normalised || au || ||
|| aamod_smooth || SPM5 smooth || wau || ||
Line 180: Line 224:
|| 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 || ||
|| 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 ||  || ||
|| aamod_slicetiming || SPM5 slice timing ||  || ||
|| aamod_realign || SPM5 realignment || a || ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || a || ||
|| aamod_norm_noss || SPM5 normalisation/segment || a || ||
|| aamod_norm_write || SPM5 write normalised || a || ||
|| aamod_smooth || SPM5 smooth || wa || ||
|| aamod_firstlevel_model || SPM5 first level model || swa || ||
|| aamod_firstlevel_contrasts || SPM5 contrasts || swa || ||
|| aamod_secondlevel_model || SPM5 second level (RFX) model || ||  ||
Line 205: Line 249:
|| 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_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 || ||  ||

Include(AutomaticAnalysisTopbar)



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.

Recipes that are available

These apply to 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

aamod_study_init

Initialise study

aamod_newsubj_init

Make subject directory

aamod_converttmaps

Convert real time t statistic outputs

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

aamod_copystructural

Structural dicom to nifti and copying

aamod_tsdiffana

Run tsdiffana

aamod_realign

SPM5 realignment

aamod_convertfieldmaps

Convert fieldmaps

aamod_fieldmap_undistort

Fieldmap undistort v4

r

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

ur

aamod_norm_noss

SPM5 normalisation/segment

ur

aamod_norm_write

SPM5 write normalised

ur

aamod_smooth

SPM5 smooth

wur

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

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

aamod_realign

SPM5 realignment

aamod_slicetiming

SPM5 slice timing

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

a

aamod_norm_noss

SPM5 normalisation/segment

a

aamod_norm_write

SPM5 write normalised

a

aamod_smooth

SPM5 smooth

wa

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

aamod_realign

SPM5 realignment

aamod_slicetiming

SPM5 slice timing

r

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

r

aamod_norm_noss

SPM5 normalisation/segment

ar

aamod_norm_write

SPM5 write normalised

ar

aamod_smooth

SPM5 smooth

war

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

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

aamod_realign

SPM5 realignment

aamod_slicetiming

SPM5 slice timing

r

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

ar

aamod_norm_noss

SPM5 normalisation/segment

ar

aamod_norm_write

SPM5 write normalised

ar

aamod_smooth

SPM5 smooth

war

aamod_firstlevel_model

SPM5 first level model

swar

aamod_firstlevel_contrasts

SPM5 contrasts

swar

aamod_secondlevel_model

SPM5 second level (RFX) model

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

aamod_study_init

Initialise study

aamod_newsubj_init

Make subject directory

aamod_converttmaps

Convert real time t statistic outputs

aamod_convertfieldmaps

Convert fieldmaps

aamod_copystructural

Structural dicom to nifti and copying

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

aamod_tsdiffana

Run tsdiffana

aamod_realign

SPM5 realignment

aamod_fieldmap_undistort

Fieldmap undistort v4

r

aamod_slicetiming

SPM5 slice timing

ur

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

aur

aamod_norm_noss

SPM5 normalisation/segment

aur

aamod_norm_write

SPM5 write normalised

aur

aamod_smooth

SPM5 smooth

waur

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

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

aamod_realign

SPM5 realignment

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

aamod_norm_noss

SPM5 normalisation/segment

aamod_norm_write

SPM5 write normalised

aamod_smooth

SPM5 smooth

w

aamod_firstlevel_model

SPM5 first level model

sw

aamod_firstlevel_contrasts

SPM5 contrasts

sw

aamod_secondlevel_model

SPM5 second level (RFX) model

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

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_convertspecialseries

Convert special series

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

aamod_realignunwarp

SPM5 realign and unwarp

aamod_slicetiming

SPM5 slice timing

u

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

au

aamod_norm_noss

SPM5 normalisation/segment

au

aamod_norm_write

SPM5 write normalised

au

aamod_smooth

SPM5 smooth

wau

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

aamod_slicetiming

SPM5 slice timing

aamod_realign

SPM5 realignment

a

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

a

aamod_norm_noss

SPM5 normalisation/segment

a

aamod_norm_write

SPM5 write normalised

a

aamod_smooth

SPM5 smooth

wa

aamod_firstlevel_model

SPM5 first level model

swa

aamod_firstlevel_contrasts

SPM5 contrasts

swa

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

CbuImaging: AutomaticAnalysisRecipes (last edited 2013-03-07 21:23:02 by localhost)