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| These apply to the development version, soon to be released (Sep 2006). |
These apply to the development version (aa_ver1_devel), soon to be released. || aarecipe_general_ver02.m || Default recipe without model || || aarecipe_general_withmodel_ver01.m || Default recipe with model || || aarecipe_general_withundistort_ver02.m || Default recipe with undistort and 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 || |
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| || 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_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 || || |
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| Slice timing first, with model |
Default recipe with model |
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| || 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_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 || || |
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| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || aamod_secondlevel_model || SPM5 second level (RFX) model || || == aarecipe_general_withundistort_ver02.m == Default recipe with undistort and 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 || 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 || || |
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| Recipe without slice timing. Suitable for sparse imaging, or when you are going to but event derivatives in your model. |
Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. |
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| || 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_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 || || |
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| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || 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 || || |
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| || 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_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 || || |
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| || 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_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 || || |
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| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
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| || 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)
Contents TableOfContents
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 the development version (aa_ver1_devel), soon to be released.
aarecipe_general_ver02.m |
Default recipe without model |
aarecipe_general_withmodel_ver01.m |
Default recipe with model |
aarecipe_general_withundistort_ver02.m |
Default recipe with undistort and 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_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
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 |
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_general_withundistort_ver02.m
Default recipe with undistort and 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 |
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 |
|
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 |
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_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 |
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 |
|