1683
Comment:
|
7772
|
Deletions are marked like this. | Additions are marked like this. |
Line 1: | Line 1: |
= Automatic Analysis Recipes = | ## page was renamed from AutomaticAnalysis [[Include(AutomaticAnalysisTopbar)]] ---- ''' Contents ''' [[TableOfContents]] ---- = Recipes that are available = |
Line 4: | Line 12: |
== Issues === Order of slice timing and motion correction === Slice timing correction involves resampling through time but not moving images, while motion correction involves moving images relative to each other. There is no simple answer to which should be done first. If slice timing is done first, then if there are abrupt movements between scans, the interpolation across time will be blurring across voxels from different parts of the brain in its correction. If motion correction is done first, then the slices in the image no longer always correspond to order of acquisition of the slices. |
This first section describes available recipes. The next section discusses issues that might help you choose the appropriate one for you. |
Line 8: | Line 14: |
If you use an interleaved slice order during acqusition (no longer the default at the CBU - see [http://imaging.mrc-cbu.cam.ac.uk/imaging/TipsForDataAcquisition#head-050cc11391e60b6442119a9e05cb0936e1659bf1 discussion of slice order] then you will probably want to apply slice timing before motion correction. Because all of the odd-numbered slices are acquired first, and the all the even ones, adjacent slices are acquired apart in time (0.5 * TR = around a second). A shift in the image by motion correction of 1 slice (4 mm) will cause a substantial shift in acqusition time for a particular slice, and slice timing will not be at all appropriately applied. | == aarecipe_general_ver02.m == Default recipe without model |
Line 10: | Line 17: |
If you use a sequential slice order during acquisition, many people prefer to apply motion correction before slice timing. I do not know if this has been evaluated in any thorough way. | === 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 |
Line 12: | Line 40: |
=== Slice timing or not? === Some people prefer to not use slice timing, and instead, to put temporal derivatives and |
=== 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. |
Include(AutomaticAnalysisTopbar)
Contents TableOfContents
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.