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| ''' Contents ''' [[TableOfContents]] | ''' Contents ''' <<TableOfContents>> |
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| = 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. |
= 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 [[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 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.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 || 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.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] || |
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| || ''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 || |
|| ''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] || |
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| Slice timing first, with model |
Default recipe with model |
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| || ''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 || || |
|| ''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.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 || u || [previous] || || aamod_norm_noss || SPM5 normalisation/segment || aur || [previous] || || aamod_norm_write || SPM5 write normalised || aur || [previous] || || aamod_smooth || SPM5 smooth || waur || [previous] || |
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| Recipe without slice timing. Suitable for sparse imaging, or when you are going to but event derivatives in your model. |
Recipe without slice timing. Suitable for sparse imaging, or when you are going to put column derivatives in your model. |
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| || ''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 || || |
|| ''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] || |
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| || ''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 || |
|| ''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] || |
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| || ''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 || || |
|| ''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] || |
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| || ''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? == The “slice-timing” problem refers to the fact that, with a continuous descending EPI sequence for example, the bottom slice is acquired TA~=TR seconds later than the top slice. If a single basis function (such as a canonical HRF) were used to model the response, and onset times were specified relative to the start of each scan, the data in the bottom slice would be delayed by TR seconds relative to the model. This would produce poor (and biased) parameter estimates for later slices, and mean that different sensitivities would apply to different slices. One solution to this problem is to interpolate the data during preprocessing as if the slices were acquired simultaneously. This works reasonably well for TRs around 3 seconds (see http://www.mrc-cbu.cam.ac.uk/~rh01/henson-1999-hbm-slice.pdf). However, a problem with slice-timing correction is that the interpolation will alias frequencies above the Nyquist limit 1/(2TR). Ironically, this means that the interpolation accuracy decreases as the slice-timing problem (ie TR) increases. For longer TRs, the severity of the interpolation error may depend on whether appreciable signal power exists above the Nyquist limit (which is more likely for rapid, randomised event-related designs). Rapid, uncorrected movements will also cause errors in the interpolation, even for short TRs. For these reasons, some people prefer an alternative solution to the slice-timing problem, which is keep the data unchanged, but have a more complex model, ie to accommodate the timing errors within the GLM. One can add the temporal derivatives of one's temporal basis functions for example, to "mop up" latency differences between slices (see http://www.mrc-cbu.cam.ac.uk/~rh01/henson-1999-hbm-slice.pdf). SPM's temporal derivative of its canonical HRF can handle latency differences of approx +/-1s for example, making it sufficient for TRs of up to 2s, if the model is synchronised with the middle slice (and if all brain regions exhibited a canonical response). If one suspects additional latency differences owing to variations in the vasculature of different brain regions, then even more basis functions may be required. Note that if you choose to add a further regressor representing temporal derivative of an assumed HRF, this will reduce the residual error and hence improve statistics for 1st-level analyses, but will not necessarily affect 2nd-level analyses on the assumed HRF alone (since basis functions are normally orthogonal to one another, in which case the parameter estimate for the assumed HRF is unchanged by the additional of its derivative). Instead, one can include (contrasts of) the parameter estimates for the temporal derivative in 2nd-level analyses as well, and make inferences using F-contrasts (or one can combine the parameter estimates to get a "latency-independent" amplitude estimate, accurate up to the time-shift of the derivative http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15110015&query_hl=1&itool=pubmed_docsum). Finally, note that in some designs with very short, fixed SOAs (<~2s), the use of a temporal derivative may not be advisable, because its associated regressor will become highly correlated with the differences between different event-types (ie one will be unable to distinguish latency differences from amplitude differences). == 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. 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. A disadvantage of doing motion correction before slice timing is that an extra reslicing stage is required in between. 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. == Realign and unwarp or just realign? == Jesper Anderson wrote a tool that models how the brain changes in shape with small motions due to distortion in the image. If there are substantial distortions in your images this may be useful. However, unless you are testing patients with clips, or have some other reason to expect distortions, this tool is probably not vital. == Normalisation using segement == By default, normalisation is now performed using the semgent tool. == AA 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. |
|| ''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.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] || |
This 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
Contents
Contents
- Considerations when choosing a recipe
-
Recipes that are available in aa version 2 devel (launch with aa_ver2_devel)
- aarecipe_dualecho_noslicetiming_ver01.m
- aarecipe_general_noreslice_ver00.m
- aarecipe_general_ver02.m
- aarecipe_general_withmodel_ver01.m
- aarecipe_general_withundistort_ver02.m
- aarecipe_noslicetiming_withmodel_ver00.m
- aarecipe_notfmri_ver01.m
- aarecipe_realignunwarp_nomodel_ver00.m
- aarecipe_slicetimingfirst_withmodel_ver00.m
- aarecipe_structuralsonly_ver00.m
-
Recipes that are available in aa version 2.0 (launch with aa_ver20)
- aarecipe_dualecho_noslicetiming_ver01.m
- aarecipe_general_noreslice_ver00.m
- aarecipe_general_ver02.m
- aarecipe_general_withmodel_ver01.m
- aarecipe_general_withundistort_ver02.m
- aarecipe_noslicetiming_withmodel_ver00.m
- aarecipe_notfmri_ver01.m
- aarecipe_realignunwarp_nomodel_ver00.m
- aarecipe_slicetimingfirst_withmodel_ver00.m
- aarecipe_structuralsonly_ver00.m
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 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.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 |
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.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 |
|
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 |
|
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.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 |
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.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 |
|
[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] |
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.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] |