[[Include(AutomaticAnalysisTopbar)]] ---- ''' Contents ''' [[TableOfContents]] ---- = New in development version = == Option to pick only last structural when there are multiple MPRAGEs == Put this in your user script aap.options.autoidentifystructural_chooselast=1; == Additional parameters can be passed to realignment/slicetime correction == '''Description:''' You can now pass extra parameters to aamod_realign and aamod_slicetiming via the aap.spmanalysis fields: || || || ||aap.spmanalysis.reslicewhich || % 0 = do not reslice any image (CBU default)|| || || % 1 = do not reslice first image (if realigned to first)|| || || % 2 = reslice all images (e.g, if want to perform slicetiming after realignment)|| ||aap.spmanalysis.writemean || % 1 = write mean (default), 0 = do not|| ||aap.spmanalysis.refslice || % reference slice for slicetiming correction (CBU default=1)|| Also, more of the standard SPM defaults apply to aamod_realign (rather than being hard-coded in aamod_realign). '''Authors:''' Rik Henson, Doris Eckstein == Changed source of EPI file prefix == Previously, a single parameter allowed changing of the EPI file prefixes that were looked for, so that slice timing could be included or not. This was the aap.directory_conventions.forrealign_fileprefix, which as either 'f' for no slice timing or 'af' if slice timing was used. It was appended by realign and all subsequent modules. This did not allow much flexibility for other stages to be included (e.g., realign & unwarp, which adds 'u') or for slice timing to be shifted to after realignment. I have now moved the file prefixes to the 'tasklist' parameter list, which is where it really belongs. Instead of one long list, tasks are now added using the new aas_addtask command. For stages that take EPI input, the aas_addtask command can optionally include a third parameter that specifies the prefix of the EPIs for this stage. So, a section of a typical tasklist specification ends looks like this: ''aap=aas_addtask(aap,'aamod_realignunwrap','f'); aap=aas_addtask(aap,'aamod_slicetiming','uf'); aap=aas_addtask(aap,'aamod_coreg_noss','auf'); aap=aas_addtask(aap,'aamod_norm_noss','auf'); aap=aas_addtask(aap,'aamod_norm_write','auf'); aap=aas_addtask(aap,'aamod_smooth','wauf'); '' Hopefully, this provides much more flexibility for stage reordering, or additional stages. == Changed .mat file for normalisation == '''Description:''' Changed name of _sn.mat and _sn_inv.mat files produced by normalisation to ms* instead of s* to reflect their origin in second pass '''Author:''' Doris Eckstein == New recipes == The default processing stream has changed in the new "general" recipes, with slice timing now AFTER realignment. This is thought to be better if slices have been acquired in a sequential rather than interleaved order. The files have also been tidied up. There is a full description of the recipes and of some issues in choosing an appropriate recipe on this new page AutomaticAnalysisRecipes. == Conversion of aribitrary special series == New aa mechanism for converting arbitrary series: - add fifth parameter to aas_addsubject command specifying series to be converted - use recipe aarecipe_notforfmri_ver00 They'll be converted and put in [subjectdir]/specialseries See example in /imaging/local/spm/aa/aa_ver1_devel/examples/aa_user_notforfmri.m '''Author:''' Rhodri Cusack = New in version 1.1 = Thanks to Danny Mitchell, Rik Henson, Matt Davis & Adam Hampshire, who all contributed to this release. You may download a PDF of a brief introduction given at the IIG on 5 June 2006 here: http://www.mrc-cbu.cam.ac.uk/~rhodri/aa/iig_may2006_aanewfeatures.pdf == tsdiffana added to pipeline == '''Description:''' This was removed in the SPM5 aa ver 1. It has been added back in. tsdiffana time series variance tool run by default, output saved to "diagnostic_aamod_tsdiffana.jpg" '''Components:''' aamod_tsdiffana ''Authors:'' DM == normalisation using segment == '''Description:''' In SPM5, the "segment" tool can be used to normalise, and has been reported to work better. However, we found it to be unstable on our structural images, due an inhomogeneity in brightness across them, a probably result of spatial variations in sensitivity in the 12 channel coil we are using. So, this version implements a two pass process: a first pass to correct the inhomogeneity, and a second pass to do the normalisation. '''Components:''' aamod_norm_noss, aamod_norm_write ''Authors:'' RH, DM, RC == support for sparse imaging == '''Description:''' Interpolation across time in slice timing makes no sense with sparse imaging, where scans are far apart. This recipe has this stage removed. '''Components:''' minor changes to modules, new recipes ''Authors:'' MD == aa_report == '''Description:''' Produces an HTML summary of various diagnostic images. This tool is still under development. '''Components:'''aa_report ''Authors:'' RC == second level statistics == '''Description:''' This module trawls through your first level analyses and generates second level analyses of a one sample t-test for each first level contrast found. The contrast names and order must the same for all subjects or an error will be given. '''Components:''' aamod_model_secondlevel ''Authors:'' RC, RH == first level statistics == '''Description:''' This sets up a model for the single subject, first level event modelling. You will need to make a copy of this module to your aa directory and modify it to specify the particular design you ran. See the aa website for instructions on how to modify it. '''Components:''' aamod_model_firstlevel ''Authors:'' AH, RC == first level contrasts == '''Description:''' Runs contrasts on each subject at the first level. You will need to make a copy of this module to your aa directory and modify it to specify the particular design you ran. See the aa website for instructions on how to modify it. '''Components:''' aamod_contrasts ''Authors:'' AH, RC == modified shell calls so that it works in desktop == '''Description:''' When the Matlab Desktop is used with Matlab 6+7, an error is generated at the top of all shell calls (see http://www.mathworks.com/support/solutions/data/1-18DNL.html?solution=1-18DNL ). I've replaced all "unix" calls in the Matlab code with a call to a new wrapper script, aas_shell. This traps the error, taking off all lines that start with tcsh: from the top of the response. I did it this way to avoid the complication of having people change their .cshrc file. '''Components:''' aas_shell ''Authors:'' RC = New in version 1.0 = 2006/2/14 [Siemens data/ SPM5/ Nifti-1 data format] == new recipes, in "examples" directory, including the following == aa_user_general_ver01 no skull stripping; uses segment not normalise [some problems have been reported with this route, if the structural fails to coregister properly with the template in the initial affine registration stage of segment. If you use it, make sure you check the final warped images are well registered with the MNI template] aa_user_general_ver00 automatic TR detection == Automatic identification and processing of realtime T maps by default == == aas_addsubject command to make it easier to tie up subject name and session numbers by eye == == wildcards now allowed when specifying subject names == == NIFTI-1 neuroimaging data format used throughout == == Conversion from Siemens DICOM data format by default; pvconv.pl, ana4dto3d no longer used == == Recognises MPRAGE and GRE_FIELDMAPPING for anatomical and fieldmap data == == Execution times stored by default. aa_benchmark command displays a summary. == == No fieldmap undistortion at present == = New in version 0.5 = 2006/2/14 [Bruker data/ SPM2/ Analyze data format] == benchmarking facility - after you've run an analysis type aa_benchmark or aa_benchmark('study path') to get a breakdown of execution times == == if more than one structural is present in the central store matching the subject name, the first is now chosen == = New in version beta 0.4 = 2004/12/3 I've released a new version of aa and made it the default at the CBU. See the note below about tsdiffana if you're going to re-run an old analysis user script with this new version. The new diagnostic jpegs make it easy to follow through how your automatic SPM analysis has gone. I hope this is useful! Rhodri ***aa beta 0.4: NEW FEATURES * added automatic saving of parameters sets and version number * added automatic saving of automatically identified series so that re-running is faster * added system for modifying CBU SPM defaults from within your user script with lines like aap.spm.defaults.normalise.write.vox=[3 3 3]; * improved error trapping for problems with pvconv.pl: now spots "not reconstructed" error and quits with a warning at this stage * added copying of .mat file during skull stripping * fixed problem so that if one subject is forcefully re-run (by deleting "done" flag) only this subject and not all the others will be run on subsequent stages * added new generation of diagnostic JPEG files as listed below. * added tsdiffana to processing pipeline Note that due to the addition of tsdiffana early in the pipeline, if you run an old aa_user script with the new version, it will rerun all stages after tsdiffana (e.g., most of the analysis). If you don't want this, either use the old version of aa by launching it with >> aa_ver0.3_beta or add the following line to your aa_user script: % list of tasks to perform (no tsdiffana) aap.tasklist.stages={'aamod_study_init','aamod_newsubj_init','aamod_copyfieldmaps', ... 'aamod_pvconv', 'aamod_copystructural','aamod_ana4dto3d', ... 'aamod_slicetiming','aamod_realign','aamod_undist','aamod_coreg', ... 'aamod_norm','aamod_undist_reslice'}; Thanks to Andy Lee for help with some of these features. ***DIAGNOSTIC JPEGS Name/ File directory/ Description diagnostic_aamod_ana4dto3d_rawmean Session raw mean as generated by ana4dto3d diagnostic_aamod_ana4dto3d_rawvar Session raw variance as generated by ana4dto3d diagnostic_aamod_tsdiffana Session output from tsdiffana diagnostic_aamod_realign Subject realignment display from SPM diagnostic_aamod_undist Subject evaluation of undistortion. Top pair of images are in distorted space and should be similar in shape and coregistered with each other. Left is distorted fieldmap magnitude, right is raw EPI. Bottom two images are in undistorted space and should be similar in shape and coregistered with each other, although not necessarily with the top two images. diagnostic_aamod_coreg Subject SPM output from coregistration of structural and undistorted EPI diagnostic_aamod_norm Subject SPM output from normalisation New in version beta 0.3 2004/11/9 PROBLEMS & FIXES (1) Problem in automatically identifying sessions in some datasets. This was due to an error message displayed by pvshow.pl. I've made the scripts handle these error messages more elegantly - you now get a warning but processing continues. If it can't find the sessions an error will still be generated. (2) The slice timing was set incorrectly in the default recipe, to 0.076 instead of 0.05. I'm sorry for this one - I've corrected it. This will effect rapid event-related designs in particular. Thanks to Andy Lee for spotting this.