CamBA / News: Recent posts

CamBA 3.0.0 is released today.

It features a new report output for CGLM and CANOVA. This report was worked on by multiple peoples for more than a year. Special thank you goes to Dr Sanja Abbott, Dr Anna Barnes and Prof John Suckling for their inputs.

This release also crushed an important bug with CGLM's output where the NifTI file cglm_clustertest.nii might not match that reported by the log file. See bug 3474937 (https://sourceforge.net/tracker/?func=detail&aid=3474937&group_id=161344&atid=819459) for more detail.... read more

CamBA 2.3.0 is updated to revision 2.3.0.20110104. It is a bug fix.

In particular, for first level pipeline, nifti_tool appears not to be working for some newer Linux distributions that are becoming main stream. The software is updated for them, with workaround for older distribution (i.e., unzip camba.cli.alternate-2.3.0.20110104-linux.zip inside camba-2.3.0 directory.

Another important fix is for first level pipeline to handle slice_code correction and dummies removal. Previously, a 'rm' instruction was wrongly issued as 'mv'.... read more

unzip the file 2.1.0_2.2.0_2.3.0/brainwaver-2.1.0.20100809.zip inside your camba directory

Bug : 2992330

hurst pipeline update patch (hurst-update.20100426.zip) corrects a problem with Hurst New Wizard Dialog. Specifically, if you did not change 'Number of Dummies' field,the pipeline will not run. It will stop at clipdummies.

Technically, the reason is the wrong initialization of number of dummies, i.e., to -1 instead of 0.

This update corrects it.

This update is labeled as optional because the new convention is to use the last power-of-2 time points. In practice, it means we have to clip leading dummies and therefore the user has to alter 'Number of dummies' field in the wizard dialog. That will make the bug disappear, even if you reset it to zero.

Bug 2895329 (https://sourceforge.net/tracker/?func=detail&aid=2895329&group_id=161344&atid=819459) [Disabling Pipeline Scheme] and Bug 2895325 (https://sourceforge.net/tracker/?func=detail&aid=2895325&group_id=161344&atid=819459) [potentially wrong parameter combination for CGLM] is so serious that it warrant an immediate correction.

Normally, I would had up the version number to 2.4.0. However, we have a few crucial users for CamBA 2.3.0 that the decision was to correct CamBA-2.3.0. ... read more

The new zip file camba-addons/2.3.0/fsl-spgr.zip give you a pipeline designed to separate White/Gray/CSF matter from a T1 image. It is designed for the so-called SPGR image.
Please note that you do need to download FSL separately from http://www.fmrib.ox.ac.uk/fsl and install it as camba-2.3.0/plugins/uk.ac.ox.fmrib.fsl/software/fsl

Please find attached updates to CGLM pipeline and Hurst Pipeline. The changes are

CGLM: Extra regressors are now double value instead of integer. Also, there is no min/max range restriction as in previous

Hurst: You can now attached RETROICOR to two location in the preprocessing.

To download this from sourgeforge.net, do camba-addon->camba-2.3.0/camba-pipelines-update.zip

We had completed the SUN SGE Engine implementation for CamBA.

To use it, download gfx-sge.zip and unzip it inside your camba-2.3.0 directory. Then restart CamBA. You now have Run->Run with SGE... menu item. This works exactly like Run->Run menu item you are familar with.

WBIC users please make sure you download gfx-sge-wbic.only.zip as well. This download loads WBIC's SGE specific setting into the SGE Engine Run dialog.... read more

CamBA is pleased to announce that by installing a newly developed plugin which is available at this site under camba-addons/2.3.0/, users can now use PPSS Engine (see http://code.google.com/p/ppss\) to process their data.

CamBA is pleased to announce that by installing a newly developed plugin which is available at this site under camba-addons/2.3.0/, users can now use PPSS Engine (see http://code.google.com/p/ppss\) to process their data.

CamBA is a Linux package for statistical analysis, by script/GUI, of neuroimaging data (fMRI/sMRI), developed at the Brain Mapping Unit, University of Cambridge. Non-parametric permutation-based statistics. Input images: 4D NiFTI files, output: HTML/PNG.

After nearly one year, the latest version of CamBA, version 2.3.0 is released.

For the majority of users this is simply a fine-tuning release of CamBA. However, for those more adventurous there are new programs, such as RETROICOR that are implemented for experiment/testing.

This is essentially a maintenance release to incorporate important bug fixes.

fixed bugs :
- CGLM not ignoring extra regressor (bug 1919626)
- CGLM "covary by total volume is now working (bug 1902986)

Some medium priority updates are push out today:

(1)CGLM now writes extra regressors into "Model" file. Previously it does not do that, causing CGLM to ignore the extra regressors
(2)Reinstates "Import from 1st Level Analysis..." for CGLM

Please also note the change of filename convention from

camba-<version>-linux[-test|-complete].zip

to
camba-<version>.<release.date>-linux[-test|-complete].zip

CamBA dataBase (CdB) is updated for camba-2.1.0. This release corrects two major problems:
(1)The menu CdB is working now
(2)When importing data into First-Level pipelines, it will now choose the NifTI file with the shortest name. This prevent <name>Remean.nii etc from being selected instead of <name>.nii

CamBA 2.1.0 does not actually create the hurst pipeline scripts correctly because of a problem with the pipeline file. It is corrected now (24 Jan 2008)

Changes is restricted to replacing hurst.pml with a new updated version.

See http://sourceforge.net/tracker/index.php?func=detail&aid=1879034&group_id=161344&atid=819459 for more information

CamBA 2.1.0 Released.

This version contains the updated user interface. Most of the changes are cosmetic. For example, changing the name of parameter values of TSAfx to make it clearer/more intuitive. More significant modification of the UI is documented later in this news item.

It uses the same version of camba programs as in CamBA 2.0.0.

Changes:
(1)You can only have one extra regressor for CANOVA. The regressor can only take on two values
(2)After your pipeline is created by CGLM wizard, it will ensure that the only valid parameter values and valid parameters are available to you.
(3)Interaction parameter in CGLM (where applicable)is now a binary switch between yes/no

This new version of BrainwaverFX works with CamBA 2.0.0 and a forthcoming (next week) CamBA 2.1.0.

To use it, on the command line, run
cd /path/to/camba-2.1.0
unzip /path/to/brainwaver-2.1.0.zip

Please read the installation instruction in
Help Menu->Help Contents->R plugin->installation
Help Menu->Help Contents->Brainwaver->installation

to properly setup brainwaver.

CamBA 2.0.0 is available for download.

This release is launched as part of our contribution to celebrate the launch of The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC, www.nitrc.org) by our friends and colleagues in the United States.

This copy of CamBA should works better with newer operating system, e.g. fedora core 6.

Changes that you will notice:
(1)First Level Wizard now ask whether you want to remove leading dummies and the slice order.... read more

A DMG file for MacOSX (Intel), based on CamBA 1.3.2 is released.

Not all CamBA components works on MacOSX. Two major thing that does not work are (1)First Level Pipelines and (2)"Pipeline Schemes". The former is omitted from this package, the latter is still on the user interface, but should not be used.

At present, it is not likely that a MacOSX port of CamBA will be created and maintained due to insufficient resources. Anyone seriously using CamBA on Mac are advised to use either Bootcamp or Virtual Machine to run the Linux version.

New Add On (extensions) packages available for CamBA:
* Brainwaver extensions or BrainwaverFX. Sophie Achard's Brainwaver package. See http://www.google.co.uk/url?sa=t&ct=res&cd=1&url=http%3A%2F%2Fcran.r-project.org%2Fsrc%2Fcontrib%2FDescriptions%2Fbrainwaver.html&ei=bm3pRoeiJ6i80wSz_6DUBg&usg=AFQjCNGs97R_d0LvaHOrg0C24vHeCmeBlA&sig2=uB3Vxp3s3pVP9wgXV5k70g
* TBSS extension (TBSSfx). This is a FSL's TBSS pipeline as they are used in Brain Mapping UNIT. The aim was to simplify TBSS processes.
* CamBA DB Extension. A set of CamBA DB directory management function and integration into CamBAfx... read more

CamBA 1.3.2 released.

New in this release:
(1)Updated New Wizards for Group Mapping Analysis, CGLM and Canova pipeline
(2)A more robust standard space algorithm
(3)A toolbar for common task
(4)More context sensitive Run->Run (and Run button) where it is only activated if you have at least one task
(5)Up/down/top/bottom button to rearrange your Input Table
(6)Sorting Input Table and for CGLM/Canova, import data from first level pipelines
(7)New first level pipeline "Conjunction"... read more

This revision is a minor update. CGLM and CANOVA are untouched. TSAFX has the +ve and -ve clusters display merged into one single HTML output. No update to UI display.

The security alert on JVM included in jre, i.e., about remote exploitation via the web is still in force. However, at present, I am not aware of any plugin that uses the web.

CamBA 1.3.0 is released.

New in this release:
* HTML output for Atlas Labeling is finally correct and consistent
* TSAFX now output activation region data as well.
* TSAFX has another pipeline scheme, i.e. "Subject spatial smoothing and response estimation". Designed to repeat analysis with different spatial smoothing
* TSAFX's median image, cluster statistics significance test and reslice are updated.
* CGLM has more options... read more

CamBA 1.2.0 is released on 28 Nov 2006.

Existing CamBA 1.1.0 pipeline should work without modification in CamBA 1.2.0. We do, however, recommend reprocessing of TSAfx pipeline to take advantage of update to standardspace program.

New in this release:
Hurst pipeline and generic pipelines for CGLM and CANOVA

We also updated standardspace in TSAfx pipeline and the program cglm for CGLM pipelines.

There is no change to the UI.

CamBA 1.1.0 is released. This release reverted the movement correction algorithm to the old, well tested (>5 years) and trustworthy one. We are investigating the existing movement correction algorithm for CamBA 1.0.0 for robustness.

Other than that, we have mainly user interface improvement:

- The parameter button is now part of the "More Action" pull down box.

- "Import Data" in the same pull down box allows you to import Input Table data from another pipeline... read more