IDAgeSexFMRI1_Loc_Con_LDeasy_LDhard 0229f90952_7_6_4_5
AA2262020-12-01 10:42:42JohanCarlinAA deprecated woo2252016-01-12 17:40:45TiborAuer2242016-01-12 17:37:46TiborAuer2232016-01-12 17:37:25TiborAuer2222016-01-12 17:33:08TiborAuer2212016-01-12 17:32:26TiborAuer2202016-01-12 17:32:15TiborAuer2192016-01-12 17:31:40TiborAuer2182016-01-12 17:31:21TiborAuer2172016-01-12 17:29:11TiborAuer2162016-01-12 17:27:56TiborAuer2152016-01-12 17:23:54TiborAuer2142016-01-12 17:23:35TiborAuer2132016-01-12 17:21:50TiborAuer2122015-03-25 15:14:31TiborAuer2112015-03-25 15:13:22TiborAuer2102015-03-25 15:12:19TiborAuer2092015-03-25 15:10:04TiborAuer2082014-02-04 12:14:55TiborAuer2072014-02-04 12:14:20TiborAuer2062014-02-04 12:12:45TiborAuer2052013-12-19 09:52:08TiborAuer2042013-11-28 15:29:57TiborAuer2032013-11-28 15:21:03TiborAuer2022013-11-28 15:19:44TiborAuer2012013-11-28 15:19:23TiborAuer2002013-11-28 15:17:29TiborAuer1992013-11-28 15:16:34TiborAuer1982013-11-28 15:13:06TiborAuer1972013-11-28 15:12:19TiborAuer1962013-11-28 15:07:57TiborAuer1952013-11-28 15:04:32TiborAuer1942013-11-28 15:02:59TiborAuer1932013-11-25 14:24:51TiborAuer1922013-11-25 14:23:28TiborAuer1912013-11-25 14:21:49TiborAuer1902013-11-25 14:20:14TiborAuer1892013-11-25 14:18:55TiborAuer1882013-11-25 14:17:59TiborAuer1872013-11-25 14:16:33TiborAuer1862013-11-25 10:39:34TiborAuer1852013-11-21 17:03:17TiborAuer1842013-11-21 16:59:19TiborAuer1832013-11-21 16:55:49TiborAuer1822013-11-21 16:54:28TiborAuer1812013-11-21 16:54:06TiborAuer1802013-11-21 16:53:04TiborAuer1792013-11-21 16:51:34TiborAuer1782013-11-21 16:50:59TiborAuer1772013-11-21 16:50:29TiborAuer1762013-11-14 17:53:33TiborAuer1752013-11-14 17:51:18TiborAuer1742013-11-14 17:50:24TiborAuer1732013-11-14 17:43:25TiborAuer1722013-11-14 17:41:55TiborAuer1712013-11-14 17:41:03TiborAuer1702013-11-14 17:40:18TiborAuer1692013-11-14 17:38:35TiborAuer1682013-11-14 17:34:48TiborAuer1672013-11-14 17:33:20TiborAuer1662013-11-14 17:30:43TiborAuer1652013-11-14 17:27:15TiborAuer1642013-11-14 17:26:12TiborAuer1632013-11-14 17:25:13TiborAuer1622013-11-14 17:22:46TiborAuer1612013-11-14 17:20:36TiborAuer1602013-11-14 17:18:54TiborAuer1592013-11-14 17:18:23TiborAuer1582013-11-14 17:15:22TiborAuer1572013-11-14 17:12:49TiborAuer1562013-11-14 17:12:26TiborAuer1552013-11-14 17:08:59TiborAuer1542013-11-14 17:07:33TiborAuer1532013-11-14 16:28:24TiborAuer1522013-11-14 16:27:15TiborAuer1512013-11-14 16:26:45TiborAuer1502013-11-14 16:22:29TiborAuer1492013-11-14 16:21:58TiborAuer1482013-11-14 16:20:56TiborAuer1472013-11-14 16:19:20TiborAuer1462013-11-14 16:17:55TiborAuer1452013-11-14 16:10:36TiborAuer1442013-11-14 16:08:52TiborAuer1432013-11-14 16:07:30TiborAuer1422013-11-14 16:05:42TiborAuer1412013-11-14 16:04:42TiborAuer1402013-10-21 13:38:22TiborAuer1392013-10-21 13:37:31TiborAuer1382013-10-21 13:34:01TiborAuer1372013-10-18 16:36:45TiborAuer1362013-10-18 16:35:57TiborAuer1352013-10-18 16:35:38TiborAuer1342013-10-18 16:35:15TiborAuer1332013-10-18 16:34:56TiborAuer1322013-10-18 16:34:26TiborAuer1312013-09-11 16:40:56TiborAuer1302013-09-06 16:03:06TiborAuer1292013-09-06 16:02:04TiborAuer1282013-09-06 16:01:39TiborAuer1272013-09-06 16:01:03TiborAuer1262013-09-06 15:59:39TiborAuer1252013-09-06 15:59:09TiborAuer1242013-09-06 15:58:13TiborAuer1232013-09-06 15:57:16TiborAuer1222013-09-06 15:55:26TiborAuer1212013-09-06 15:55:04TiborAuer1202013-09-06 15:53:51TiborAuer1192013-09-06 15:53:22TiborAuer1182013-09-06 15:52:59TiborAuer1172013-09-06 15:52:32TiborAuer1162013-09-06 15:50:23TiborAuer1152013-09-06 15:49:37TiborAuer1142013-09-06 15:47:30TiborAuer1132013-09-06 15:47:05TiborAuer1122013-09-06 15:44:10TiborAuer1112013-09-06 14:57:47TiborAuer1102013-08-09 17:34:41TiborAuer1092013-08-09 17:33:34TiborAuer1082013-08-09 17:09:08TiborAuer1072013-08-09 17:08:31TiborAuer1062013-08-09 17:05:11TiborAuer1052013-08-09 17:04:24TiborAuer1042013-08-09 17:02:57TiborAuer1032013-08-09 17:02:10TiborAuer1022013-08-09 17:01:57TiborAuer1012013-08-09 17:01:31TiborAuer1002013-08-09 17:01:08TiborAuer992013-08-09 17:00:52TiborAuer982013-08-09 16:59:34TiborAuer972013-08-09 16:59:12TiborAuer962013-08-09 16:58:16TiborAuer952013-08-09 16:54:39TiborAuer942013-08-09 16:53:47TiborAuer932013-08-09 16:53:31TiborAuer922013-08-08 16:35:41TiborAuer912013-08-08 16:32:47TiborAuer902013-08-08 16:32:23TiborAuer892013-08-08 16:28:32TiborAuer882013-08-02 16:01:08TiborAuer872013-08-02 15:57:52TiborAuer862013-08-02 15:57:40TiborAuer852013-08-02 15:57:13TiborAuer842013-07-10 10:39:16TiborAuer832013-07-10 10:36:01TiborAuer822013-07-10 10:35:40TiborAuer812013-07-10 10:34:56TiborAuer802013-07-10 10:34:33TiborAuer792013-07-10 10:32:26TiborAuer782013-07-10 10:31:43TiborAuer772013-06-27 13:24:40TiborAuer762013-06-27 13:23:58TiborAuer752013-06-27 13:18:50TiborAuer742013-06-27 13:16:24TiborAuer732013-06-27 13:12:12TiborAuer722013-06-27 13:10:41TiborAuer712013-06-27 13:00:40TiborAuer702013-06-27 12:58:46TiborAuer692013-06-27 10:59:15TiborAuer682013-06-27 10:56:17TiborAuer672013-06-26 09:17:32TiborAuer662013-06-26 09:16:10TiborAuer652013-06-26 09:15:31TiborAuer642013-06-19 19:30:43TiborAuer632013-06-06 15:08:00TiborAuer622013-06-06 15:07:01TiborAuer612013-06-06 15:03:57TiborAuer602013-05-20 15:42:47TiborAuer592013-05-20 15:42:05TiborAuer582013-04-24 16:14:13TiborAuer572013-04-24 16:10:41TiborAuer562013-04-24 16:09:38TiborAuer552013-04-24 16:06:40TiborAuer542013-04-24 16:05:59TiborAuer532013-04-24 16:05:04TiborAuer522013-04-24 16:04:03TiborAuer512013-04-24 16:03:06TiborAuer502013-04-24 15:53:05TiborAuer492013-04-24 15:52:27TiborAuer482013-04-24 15:51:53TiborAuer472013-04-24 15:49:04TiborAuer462013-04-24 15:48:18TiborAuer452013-04-24 15:43:15TiborAuer442013-04-24 15:42:30TiborAuer432013-04-24 15:39:50TiborAuer422013-04-24 15:39:10TiborAuer412013-04-24 15:37:57TiborAuer402013-04-24 15:37:41TiborAuer392013-04-24 15:36:10TiborAuer382013-04-24 15:35:39TiborAuer372013-04-24 15:35:01TiborAuer362013-04-24 15:33:07TiborAuer352013-04-24 15:27:17TiborAuer342013-04-24 15:10:01TiborAuer332013-04-24 15:09:09TiborAuer322013-04-24 15:07:25TiborAuer312013-04-24 15:05:59TiborAuer302013-04-24 15:05:32TiborAuer292013-04-24 15:03:40TiborAuer282013-04-24 15:01:03TiborAuer272013-04-24 15:00:31TiborAuer262013-04-24 14:58:34TiborAuer252013-04-24 14:31:57TiborAuer242013-04-24 14:31:04TiborAuer232013-04-24 14:26:29TiborAuer222013-04-24 14:19:41TiborAuer212013-04-24 14:17:37TiborAuer202013-04-24 14:16:17TiborAuer192013-04-24 14:03:42TiborAuer182013-04-24 14:02:38TiborAuer172013-04-24 14:01:38TiborAuer162013-04-24 13:59:07TiborAuer152013-04-24 13:52:59TiborAuer142013-04-24 13:52:37TiborAuer132013-04-24 13:49:12TiborAuer122013-04-24 13:48:02TiborAuer112013-04-24 13:47:00TiborAuer102013-04-24 13:45:45TiborAuer92013-04-24 13:36:53TiborAuer82013-04-24 13:36:29TiborAuer72013-04-24 13:35:11TiborAuer62013-04-24 13:34:17TiborAuer52013-04-24 13:25:37TiborAuer42013-04-24 13:24:22TiborAuer32013-04-24 13:23:18TiborAuer22013-04-23 16:33:33TiborAuer12013-04-23 16:31:52TiborAuer
Automatic analysis (aa)Automatic analysis (aa) is a pipeline system for neuroimaging, written in Matlab. It supports SPM 5/8 and some functions from FSL. As of December 2020, AA is deprecated at CBU. The last update that was deployed at CBU is release 5.4.0_202008, which is available on the imaging system under /imaging/local/software/AA/release-5.4.0_202008. For critical errors in existing pipelines, please contact Johan Carlin for support. For new projects, please investigate alternatives such as nipype, which is available at CBU as part of the Neuroconda environment. AA continues to be developed outside of CBU, and its developers can be reached on the project Github page. The documentation below is outdated and should be read with caution. For more information see: Version 2.2 and earlier: Manual Version 4: This page GitHub
Paths to aaDifferent versions live in: legacy versions (0.1beta - 2.0) - {X} unsupported /imaging/local/spm/aa/aa-ver0.1_beta /imaging/local/spm/aa/aa-ver0.2_beta ... old versions (2.2 - 4.beta) /imaging/local/spm/aa_svn_new/versions/release-2.2 /imaging/local/spm/aa_svn_new/versions/release-3.0 ... new version (4.0 - 4.1) (based on the latest devel-share branch from GitHub) /imaging/local/software/AA/release-4.0 /imaging/local/software/AA/release-4.2 - stable /imaging/local/software/AA/release-4.2_[YYYYMM] - backups on [YYYYMM] /imaging/local/software/AA/release-4.3 - {OK} recommended
Installing aa
RequirementsOperating system: Linux only! Must-have: MATLAB: tested on versions >=r2009a. (!) In CBSU, you need r2012b for parallel computing SPM: most functions work with SPM5 and SPM8, but full functionality requires SPM12 For MEG: Neuromag (only ELEKTA systems are supported, so far)
Using aaFor a comprehensive summary, please read the latest manuscript. Please, do not forget to cite it when using!
ConfigurationBefore running aa you need to add the corresponding path to MATLAB Path: File/Set Path... (!) To avoid version conflicts make sure that it is added to the top of the Path. It is even more important that path_to_aa/extrafunctions/spm_mods is on the top (of SPM's paths), so modification to the spm may have effect.
RunningYou need a User Master Script (UMS) for fMRI User Master Script (UMS) for DARTEL User Master Script (UMS) for FreeSurfer Optionally, you can also specify your own parameter settings loaded by aarecipe. E.g.: User-specific parameter settings (you may need to change the path pointing to the "parent" xml)
Features
Parallel computingUsage To enable parallel computing you have to be logged in an appropriate computing machine (login11-14), make sure that our local MATLAB scripts for qsub (/hpc-software/matlab/cbu) is in your MATLAB path, which is there usually, but it is worth checking :), and add the following line to your UMS: (!) Because each thread will load the saved MATLAB path, it is very important that it is set and saved correctly before initiating parallel jobs. See Configuration for more information! Monitoring
Handling multiple DICOM sourcesColon-separated-list (CSL) for rawdatadir: The “old” script should work without any changes but the newer ones (based on Recent Update on 2013/09/06) should revert. When multiple sources are defined, use CSL. E.g.:
Support for NIFTI-4D imagesAs a default, NIFTI-3D is set. To enable NIFTI-4D, you have to specify it in the UMS:
Multi-level interlinked reportingLevels: Study (reporting second-level) Subjects (each subjects separately) Summaries: Subjects Registration First-level thresholded maps Usage Based on aap structure If you are in the analysis folder
Garbage collectionTidy up unnecessary files - delete any inputs to a module that are not also specified as an output. Usage: Based on aap structure If you are in the analysis folder (!) From v4.2, it is automatically performed at the end of the analysis according to aap.options.garbagecollection
"Inheritable" parameter settingsThere is an option to have site-, user-, and/or study-specific parameter settings containing only the parameters to be overridden (see example).
Non-Standard ModulesFirst-level thresholding List of significant activation maps Overlays on axial slices (T1 MNI) Rendering results in 3D FSL FreeSurfer
Advanced Features
Input fileIt is possible to specify Subjects, Sessions and Events based on a text file. Required options in aap.acq_details.input (see also aap_parameters_defaults_CBSU.xml): list: text file: Required format: a CSV file: cells are separated with semicolon subcells are separated with "_" a header in the first line Required columns (may contain more): "ID": numbers for identifying subjects "FMRI1": cells for the fMRI measurement; it must contain the same number of subcells as the coresponding column header first subcell is the CBU volunteer number (without "CBU") series numbers are defined in the consecutive subcells with the same order as their names in the coresponding column header E.g.: As "pure" text: ID;Age;Sex;FMRI1_Loc_Con_LDeasy_LDhard 02;29;f;90952_7_6_4_5 selected_sessions: subselection of a subset of series: E.g. (based on the example above): [3 4] --> LDeasy and LDhard referencedirectory_tmpl: a template for path to the folder containing Event files (.mat files in SPM-format) Required format: must contain "*" which will be substituted withID (see above) E.g.: '/imaging/ta02/ActionWords/Analysis/E-Prime/DAW*/ref' The folder should contain the regressor(s) in SPM format (.mat file) with filename format: condition_vol_ID-Session Name.mat. E.g. (based on the example above): condition_vol_2-LDeasy.mat Then you add these lines to your UMS (based on the example above):
Citing aaCusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, Peelle JE (2015). Automatic analysis (aa): Efficient neuroimaging workflows and parallel processing using Matlab and XML. Frontiers in Neuroinformatics 8:90.
Recent Updates
2013/11/25
New feature - first-level modelPrevious implementation allowed for changing only the UNITS. Now, it is possible to fully customize the basis function. The defaults are: (!) It means, however, that the old reference aap.tasksettings.aamod_firstlevel_model.UNITS has been deprecated, and aap.tasksettings.aamod_firstlevel_model.xBF.UNITS must be used instead (see UMS).
Fix - subjectnameThe most recent update fixes the correspondence of the subjectname, the name you use when adding subject in the User Master Script (USM), and the referring aap setting aap.directory_conventions.subjectoutputformat. It means that subjectname has to be provided according to the setting. The default is 'CBU%06d*', which means that you need to provide the number (as an integer, without CBU), e.g. 90952. Many of you may use part or full name of the directory, which will result an error message most likely upon aamod_evaulatesubjectnames. You have two options: Either, specify subjectname in UMS according to the setting (see above). Or, change the setting: If you use partial name (e.g. 'CBU090952'), then add this line to the UMS: If you use full name (e.g. 'CBU090952_MR09032/20090828_131456'), then add this line to the UMS:
2013/11/21 New features!"Inheritable" parameter setting aap.directory_conventions.spmtoolsdir: option to specify path for SPM tools which will be taken over when running analysis on the computing cluster. More paths can be specified using the CSL concept similarly to multiple DICOM sources
2013/10/29 New features!FreeSurfer has been tested Solving backward-compatibility for handling multiple DICOM sources (see Recent Update on 2013/09/06)
2013/09/06 New features!DATREL has been tested Improved monitoring of the parallel computing Handling multiple DICOM sources (e.g. /mridata/cbu and /mridata/camcan) Known issue (backward compatibility) SOLVED (see Recent Update on 2013/10/29): If you want to customize DICOM sources, you need to put your own path to source not into rawdatadir directly (as used to), but into rawdatadir.paths (cell array) or rawdatadir.paths{1} (cellstring).
2013/08/08 Parallel computing is workingSee Parallel computing for more information! Known bugs: Conventional SPM diagnostic will be missing for: aamod_realignunwarp (no report of fieldmaps) aamod_coreg_noss However, FSL diagnostics are unaffected.
2013/08/02 new version v4.1 (latest devel-share branch from GitHub)merge with GitHub completed release-4.1 is now the latest stable NIFTI-4D support is independent from SPM version. N.B.: Configuration!
2013/06/26 merge with the latest devel-rhodri branch from GitHubrelease-4.0 is now the latest stable
2013/06/06 new featureNIFTI-4D support added.
2013/05/13 new featureGarbage collection tested New report summary: Head movement: outlier-detection with boxplot
2013/04/24 CBSU Patch/Extension for Version 4 is availableNew features: Handling input file as a list of subjects and sessions Module for first-level thresholding Multi-level interlinked reporting: Known bugs: Parallel computing is still not working!
2013/03/03 Version 4 is availableNew features in version 4