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* Version 4: .[[AA|This page]] .[[https://github.com/rhodricusack/automaticanalysis|GitHub]] .[[https://github.com/rhodricusack/automaticanalysis/wiki|Wiki]] |
* Version 4: . [[AA|This page]] . [[https://github.com/rhodricusack/automaticanalysis|GitHub]] . [[https://github.com/rhodricusack/automaticanalysis/wiki|Wiki]] |
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Any problems, report them to [[DannyMitchell|Danny Mitchell]] or [[TiborAuer|Tibor Auer]]. | Any problems, report them to [[DannyMitchell|Danny Mitchell]] (version 2 and 3) or [[TiborAuer|Tibor Auer]] (version 4). |
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== Available versions == {{{#!highlight bash /imaging/local/spm/aa # old versions /imaging/local/spm/aa4_github # old versions /imaging/local/software/release-3.0.1 /imaging/local/software/release-4.0 /imaging/local/software/release-4.0p |
<<TableOfContents(2)>> == Paths to aa == Different 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-4.1` - {OK} '''recommended''' == Using aa == === Configuration === [[#config|]] Before running aa you need to add the corresponding path to MATLAB Path: * File/Set Path... * {{{#!highlight matlab numbers=off addpath('path_to_aa'); savepath; |
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(!) 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''', so modification to the spm may have effect. | |
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=== Running === Then, you need a [[attachment:aa_simple.m|User Master Script (UMS)|&do=get]] === Advanced Features === ==== Input file ==== It 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.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.: . {{{#!csv ID;Age;Sex;FMRI1_Loc_Con_LDeasy_LDhard 02;29;f;90952_7_6_4_5 }}} 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 with''ID'' (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): . {{{#!highlight matlab numbers=off aap.acq_details.input.list='/imaging/ta02/ActionWords/Analysis/Subject_List_Test.csv'; aap.acq_details.input.selected_sessions = [3 4]; aap.acq_details.input.referencedirectory_tmpl = '/imaging/ta02/ActionWords/Analysis/E-Prime/DAW*/ref'; aap = aas_processinput(aap); }}} |
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== 2013/04/24 CBSU Patch/Extension for Version 4 is available == Add {{{ /imaging/local/software/release-4.0p |
=== 2013/08/08 Parallel computing is working === * To enable parallel computing you have to be logged in an appropriate computing machine (login11-14) and add the following line to your UMS: . {{{#!highlight matlab numbers=off aap.options.wheretoprocess = 'qsub'; % parallel; typical localsingle |
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to the '''top''' of your MATLAB Path. | * {{{#!wiki caution '''Known bugs:''' |
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New features (apart from debugging): * Handling input file as a list of subjects and sessions |
Conventional SPM diagnostic will be missing for: * aamod_realignunwarp (only 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 . === 2013/06/26 merge with the latest devel-rhodri branch from GitHub === * release-4.0 is now the latest stable . === 2013/06/06 new feature === * NIFTI-4D support added. It works only with '''spm8_fil_r5236''' . As a default, NIFTI-3D is set. To enable NIFTI-4D, you have to specify it in the UMS: . {{{#!highlight matlab numbers=off aap.options.NIFTI4D = 1; % 4D support; typical value 0 }}} === 2013/05/13 new feature === * Garbage collection tested * New report summary: * Head movement: outlier-detection with boxplot === 2013/04/24 CBSU Patch/Extension for Version 4 is available === New features: * Handling input file as a list of subjects and sessions (see Advanced Features/Input file) |
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* Overlays on axial slices (T1 MNI) | * Overlays on axial slices (T1 MNI) |
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== 2013/03/03 Version 4 is available == | {{{#!wiki caution '''Known bugs:''' Parallel computing is still not working! }}} === 2013/03/03 Version 4 is available === |
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Add {{{ /imaging/local/software/release-4.0 }}} to your MATLAB Path. {{{#!wiki caution '''It is very buggy!''' }}} |
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.
For more information see:
Any problems, report them to Danny Mitchell (version 2 and 3) or Tibor Auer (version 4).
Paths to aa
Different versions live in:
legacy versions (0.1beta - 2.0) - 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-4.1 - recommended
Using aa
=== Configuration === #config Before running aa you need to add the corresponding path to MATLAB Path:
- File/Set Path...
addpath('path_to_aa'); savepath;
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, so modification to the spm may have effect.
Running
Then, you need a User Master Script (UMS)
Advanced Features
Input file
It 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.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
- Required format:
- 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
- Required format:
- Then you add these lines to your UMS (based on the example above):
aap.acq_details.input.list='/imaging/ta02/ActionWords/Analysis/Subject_List_Test.csv'; aap.acq_details.input.selected_sessions = [3 4]; aap.acq_details.input.referencedirectory_tmpl = '/imaging/ta02/ActionWords/Analysis/E-Prime/DAW*/ref'; aap = aas_processinput(aap);
Recent Updates
2013/08/08 Parallel computing is working
- To enable parallel computing you have to be logged in an appropriate computing machine (login11-14) and add the following line to your UMS:
aap.options.wheretoprocess = 'qsub'; % parallel; typical localsingle
Known bugs:
Conventional SPM diagnostic will be missing for:
- aamod_realignunwarp (only 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
2013/06/26 merge with the latest devel-rhodri branch from GitHub
- release-4.0 is now the latest stable
2013/06/06 new feature
NIFTI-4D support added. It works only with spm8_fil_r5236
- As a default, NIFTI-3D is set. To enable NIFTI-4D, you have to specify it in the UMS:
aap.options.NIFTI4D = 1; % 4D support; typical value 0
2013/05/13 new feature
- Garbage collection tested
- New report summary:
- Head movement: outlier-detection with boxplot
2013/04/24 CBSU Patch/Extension for Version 4 is available
New features:
- Handling input file as a list of subjects and sessions (see Advanced Features/Input file)
- Module for first-level thresholding
- List of significant activation maps
- Overlays on axial slices (T1 MNI)
- Rendering results in 3D
- Multi-level interlinked reporting:
- Study (reporting second-level)
- Subjects (each subjects separately)
- Summaries:
- Subjects
- Registration
- First-level thresholded maps
Known bugs:
Parallel computing is still not working!