AA

2013/11/25

New feature - first-level model

Previous implementation allowed for changing only the UNITS. Now, it is possible to fully customize the basis function. The defaults are:
```
aap.tasksettings.aamod_firstlevel_model.xBF.UNITS = 'secs'; 
aap.tasksettings.aamod_firstlevel_model.xBF.Volterra = 1;
aap.tasksettings.aamod_firstlevel_model.xBF.name = 'hrf';
aap.tasksettings.aamod_firstlevel_model.xBF.length = 32;
aap.tasksettings.aamod_firstlevel_model.xBF.order = 1;
aap.tasksettings.aamod_firstlevel_model.xBF.T = 17; % number of time bins per TR
aap.tasksettings.aamod_firstlevel_model.xBF.T0 = []; % slice at first time bin (empty allows for automatic setting - for both T and T0 - based on slice-time correction)
```
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 - subjectname

The 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:
  - aap.directory_conventions.subjectoutputformat = '%s*';
  - If you use full name (e.g. 'CBU090952_MR09032/20090828_131456'), then add this line to the UMS:
  - aap.directory_conventions.subjectoutputformat = '%s';

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 working

See 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 GitHub

release-4.0 is now the latest stable

2013/06/06 new feature

NIFTI-4D support added.

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
Module for first-level thresholding
Multi-level interlinked reporting: