562013-03-07 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

See the page on SliceTiming for a discussion

See the Realign Unwarp section of the MotionCorrection page.

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.

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

For dual echo (GE/SE) with undistortion but no slice timing

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_dualecho_noslicetiming_ver01 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_noreslice_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe with model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_withmodel_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_withundistort_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model.

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_noslicetiming_withmodel_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Converts structurals & special series as specified in 5th parameter of aas_addsubject command

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_notfmri_ver01 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Recipe using realign & unwarp without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_realignunwarp_ver00 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Slice timing first, with model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_slicetimingfirst_withmodel_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Recipe that only processes structurals

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_structuralsonly aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

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

For dual echo (GE/SE) with undistortion but no slice timing

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_dualecho_noslicetiming_ver01 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_noreslice_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe with model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_withmodel_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Default recipe without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_general_withundistort_ver02 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model.

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_noslicetiming_withmodel_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Converts structurals & special series as specified in 5th parameter of aas_addsubject command

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_notfmri_ver01 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Recipe using realign & unwarp without model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_realignunwarp_ver00 aap_spmanalysis_autotr_resliceall_ver00 aap_acq_details_ver00

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]

Slice timing first, with model

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_slicetimingfirst_withmodel_ver00 aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]

Recipe that only processes structurals

aap_directory_conventions_ver00 aap_options_ver00 aap_tasklist_structuralsonly aap_spmanalysis_autotr_noreslice_ver00 aap_acq_details_ver00

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]