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 |
|
aamod_newsubj_init |
aamod_copystructural |
Structural dicom to nifti and copying |
|
aamod_newsubj_init |
aamod_tsdiffana |
Run tsdiffana |
|
aamod_convert_epis |
aamod_realign |
SPM5 realignment |
|
aamod_convert_epis |
aamod_convertfieldmaps |
Convert fieldmaps |
|
aamod_newsubj_init |
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 |
|
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 |
|
[previous] |
aamod_coreg_noss |
SPM5 coregister EPI to structural without skull stripping |
|
aamod_realign |
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 |
|
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_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 |
|
aamod_newsubj_init |
aamod_convert_epis |
Performing dicom to nifti conversion of EPIs |
|
aamod_newsubj_init |
aamod_tsdiffana |
Run tsdiffana |
|
[previous] |
aamod_realignunwarp |
SPM5 realign and unwarp |
|
aamod_convert_epis |
aamod_slicetiming |
SPM5 slice timing |
u |
[previous] |
aamod_coreg_noss |
SPM5 coregister EPI to structural without skull stripping |
u |
|
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 |
|
aamod_newsubj_init |
aamod_convert_epis |
Performing dicom to nifti conversion of EPIs |
|
aamod_newsubj_init |
aamod_tsdiffana |
Run tsdiffana |
|
[previous] |
aamod_slicetiming |
SPM5 slice timing |
|
aamod_convert_epis |
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] |