|
Size: 7615
Comment:
|
Size: 8181
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 27: | Line 27: |
| || aarecipe_general_ver02.m || Default recipe without model || || aarecipe_general_withmodel_ver01.m || General with 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. || || 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 || |
|
| Line 29: | Line 35: |
| Line 38: | Line 43: |
| || 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 || || |
| Line 51: | Line 56: |
| Slice timing first, with model |
General with model |
| Line 61: | Line 65: |
| || 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 || || |
| Line 75: | Line 79: |
| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
| Line 78: | Line 82: |
| Line 87: | Line 90: |
| || 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 || || |
| Line 100: | Line 103: |
| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
| Line 103: | Line 106: |
| Line 112: | 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_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 || || |
| Line 126: | Line 128: |
| Line 135: | Line 136: |
| || 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 || || |
| Line 149: | Line 150: |
| || aamod_secondlevel_model || SPM5 second level (RFX) model || || | || aamod_secondlevel_model || SPM5 second level (RFX) model || || |
| Line 152: | Line 153: |
| Line 161: | Line 161: |
| || aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || |
|| aamod_study_init || Initialise study || || || aamod_newsubj_init || Make subject directory || || || aamod_converttmaps || Convert real time t statistic outputs || || |
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, soon to be released (Sep 2006).
aarecipe_general_ver02.m |
Default recipe without model |
aarecipe_general_withmodel_ver01.m |
General with 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. |
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
General 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 |
|