Diff for "AutomaticAnalysisRecipes" - MRC CBU Imaging Wiki
location: Diff for "AutomaticAnalysisRecipes"
Differences between revisions 49 and 50
Revision 49 as of 2007-08-31 15:47:14
Size: 13167
Editor: RhodriCusack
Comment:
Revision 50 as of 2007-08-31 15:49:38
Size: 14634
Editor: RhodriCusack
Comment:
Deletions are marked like this. Additions are marked like this.
Line 46: Line 46:
|| ''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 ||  ||
|| ''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 || || [previous] ||
|| aamod_copystructural || Structural dicom to nifti and copying || || [previous] ||
|| aamod_tsdiffana || Run tsdiffana || || [previous] ||
|| aamod_realign || SPM5 realignment || || [previous] ||
|| aamod_convertfieldmaps || Convert fieldmaps || || [previous] ||
|| 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] ||
Line 69: Line 69:
|| ''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 ||  ||
|| ''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_slicetiming || SPM5 slice timing || || [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] ||
Line 91: Line 91:
|| ''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 ||  ||
|| ''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] ||
Line 113: Line 113:
|| ''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 || ||  ||
|| ''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_slicetiming || SPM5 slice timing || r || [previous] ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || ar || [previous] ||
|| 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] ||
Line 138: Line 138:
|| ''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 ||  ||
|| ''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] ||
Line 162: Line 162:
|| ''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 || ||  ||
|| ''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] ||
Line 186: Line 186:
|| ''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 || ||  ||
|| ''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] ||
Line 201: Line 201:
|| ''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 ||  ||
|| ''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_realignunwarp || SPM5 realign and unwarp || || [previous] ||
|| aamod_slicetiming || SPM5 slice timing || u || [previous] ||
|| aamod_coreg_noss || SPM5 coregister EPI to structural without skull stripping || au || [previous] ||
|| aamod_norm_noss || SPM5 normalisation/segment || au || [previous] ||
|| aamod_norm_write || SPM5 write normalised || au || [previous] ||
|| aamod_smooth || SPM5 smooth || wau || [previous] ||
Line 223: Line 223:
|| ''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 || ||  ||
|| ''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_slicetiming || SPM5 slice timing || || [previous] ||
|| 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] ||
Line 248: Line 248:
|| ''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 || ||  ||
|| ''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] ||

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

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

[previous]

aamod_copystructural

Structural dicom to nifti and copying

[previous]

aamod_tsdiffana

Run tsdiffana

[previous]

aamod_realign

SPM5 realignment

[previous]

aamod_convertfieldmaps

Convert fieldmaps

[previous]

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

[previous]

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

[previous]

aamod_tsdiffana

Run tsdiffana

[previous]

aamod_realign

SPM5 realignment

[previous]

aamod_slicetiming

SPM5 slice timing

[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]

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

[previous]

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

[previous]

aamod_tsdiffana

Run tsdiffana

[previous]

aamod_realign

SPM5 realignment

[previous]

aamod_slicetiming

SPM5 slice timing

r

[previous]

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

ar

[previous]

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

[previous]

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

[previous]

aamod_tsdiffana

Run tsdiffana

[previous]

aamod_realignunwarp

SPM5 realign and unwarp

[previous]

aamod_slicetiming

SPM5 slice timing

u

[previous]

aamod_coreg_noss

SPM5 coregister EPI to structural without skull stripping

au

[previous]

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

[previous]

aamod_convert_epis

Performing dicom to nifti conversion of EPIs

[previous]

aamod_tsdiffana

Run tsdiffana

[previous]

aamod_slicetiming

SPM5 slice timing

[previous]

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]

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