AutomaticAnalysisRecipes562013-03-07 21:23:02localhostconverted to 1.6 markup552007-09-12 14:28:09RhodriCusack542007-09-12 14:27:35RhodriCusack532007-09-12 14:27:04RhodriCusack522007-08-31 16:04:14RhodriCusack512007-08-31 16:00:10RhodriCusack502007-08-31 15:49:38RhodriCusack492007-08-31 15:47:14RhodriCusack482007-02-15 09:53:28RhodriCusack472006-09-05 15:48:40RhodriCusack462006-09-05 15:47:01RhodriCusack452006-09-05 14:38:53RhodriCusack442006-09-05 14:38:35RhodriCusackRevert to revision 42.432006-09-05 14:32:21RhodriCusack422006-09-05 14:32:06RhodriCusack412006-09-05 14:05:49RhodriCusack402006-09-04 13:18:21devel03.mrc-cbu.cam.ac.uk392006-09-04 13:18:00devel03.mrc-cbu.cam.ac.uk382006-09-04 13:10:43devel03.mrc-cbu.cam.ac.uk372006-09-04 10:37:12RhodriCusack362006-09-04 10:35:16RhodriCusack352006-09-04 10:21:12cmbg-cache-2.server.ntli.net342006-09-04 10:16:46RhodriCusack332006-09-04 10:09:48cmbg-cache-2.server.ntli.net322006-09-04 10:08:55cmbg-cache-2.server.ntli.net312006-09-04 09:08:06RhodriCusack302006-09-01 19:49:17RikHenson292006-09-01 19:21:56RikHenson282006-09-01 19:20:25RikHenson272006-09-01 17:38:59RhodriCusack262006-09-01 17:36:42RhodriCusack252006-09-01 17:32:23RhodriCusack242006-09-01 17:20:01RhodriCusack232006-09-01 17:17:29RhodriCusack222006-09-01 17:16:40RhodriCusack212006-09-01 17:15:35RhodriCusack202006-09-01 17:14:50RhodriCusack192006-09-01 17:13:17RhodriCusack182006-09-01 17:13:09RhodriCusackRevert to revision 16.172006-09-01 17:12:25RhodriCusack162006-09-01 17:11:54RhodriCusackRevert to revision 14.152006-09-01 17:11:34RhodriCusack142006-09-01 17:11:24RhodriCusackRevert to revision 12.132006-09-01 17:10:05RhodriCusack122006-09-01 17:09:56RhodriCusackRevert to revision 10.112006-09-01 16:36:44RhodriCusack102006-09-01 16:36:27RhodriCusackRevert to revision 8.92006-09-01 16:25:03RhodriCusack82006-09-01 15:03:54RhodriCusack72006-09-01 13:46:18RhodriCusack62006-09-01 13:45:57RhodriCusack52006-09-01 13:45:02RhodriCusack42006-09-01 13:44:34RhodriCusack32006-09-01 13:43:59RhodriCusack22006-09-01 13:41:19RhodriCusack12006-09-01 13:26:25RhodriCusackThis manual is for aa parallel version 2.2 and earlier. You might prefer the new aa wiki for aa version 3.0 and above or information on cloud execution Introduction General overview File format Choosing an appropriate recipe Getting started aa parallel Parameter set reference Release notes for different versions Contents Considerations when choosing a recipeSlice timing or not?See the page on SliceTiming for a discussion Realign and unwarp or just realign?See the 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 in aa version 2 devel (launch with aa_ver2_devel) 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.mFor 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 u [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.mDefault 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.mDefault 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 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.mDefault 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 aamod_realign
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.mDefault 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 u [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.mRecipe 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.mConverts 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.mRecipe 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.mSlice 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 [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.mRecipe 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]
Recipes that are available in 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.mFor 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.mDefault 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.mDefault 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.mDefault 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.mDefault 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.mRecipe 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.mConverts 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.mRecipe 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.mSlice 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.mRecipe 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]