BrainFX Wiki
http://www.cambafx.org/wiki/
2010-07-07T03:47:12+01:00BrainFX Wiki
http://www.cambafx.org/wiki/
http://www.cambafx.org/wiki/lib/images/favicon.icotext/html2010-07-05T19:33:40+01:00Cinly Ooi (co224@131.111.87.179)CamBAfx Packaging Instructions
http://www.cambafx.org/wiki/developer/issues/packaging?do=diff&1278354820
In Nov 2007 both WBIC and BCNI updated their Linux images. Unfortunately, the GCC copy that they used, although being the same version (4.1.2), are compiled nearly one year apart and have compatibility problem. In particular, if compiled in BCNI, it...text/html2009-12-09T20:00:25+01:00Cinly Ooi (co224@131.111.87.179)standardspace - created
http://www.cambafx.org/wiki/programs/s/standardspace?do=diff&1260388825
If standardspace fails, check the following: Is the *StdMask.png OK? If not, check that *Affine.txt looks fine Diagostic Locate the dataset with problem. Copy only the image files, i.e., *Nat*.nii into a separate directory. Making sure you do...text/html2009-12-09T19:26:03+01:00Cinly Ooi (co224@131.111.87.179)CamBA Programs
http://www.cambafx.org/wiki/programs?do=diff&1260386763
Information about program we used. Non-CamBA programs are marked as such. It is not a comprehensive list and is mainly used to document experience about individual programs, rather than how they are used. Included here are also third party programs ...text/html2009-11-20T20:57:06+01:00Cinly Ooi (co224@131.111.87.179)Time Series Analysis Pipeline
http://www.cambafx.org/wiki/pipelines/tsafx?do=diff&1258750626
Processing stop at voxelsignificancetest and the error message There are problems with this program run. Please check messages above is given. Possible Reasons Data is in the wrong endian This error is known to occur when the data is in a diffe...text/html2009-11-20T20:54:52+01:00Cinly Ooi (co224@131.111.87.179)Response Estimation
http://www.cambafx.org/wiki/programs/r/responseestimation?do=diff&1258750492
Progress log will look something like this: out> cambafx.sh> Set CAMBA_PATH to '/path/to/camba-1.3.2/plugins/uk.ac.cam.psychiatry.camba.linux_1.3.2/software/camba/bin/' out> cambafx.sh> Running '/path/to/camba-1.3.2/plugins/uk.ac.cam....text/html2009-05-01T16:46:22+01:00Cinly Ooi (co224@131.111.87.179)dcmdir
http://www.cambafx.org/wiki/programs/d/dcmdir?do=diff&1241192782
Part of dcm2che Output for -t <dicomdir> option Note: <dicomdir> id the property file for the dicom directory. It is a file that looks like text with markup. Format: (gggg,eeee) MM #N [AAAA] DDDDDDDDDDDDD where gggg = group, see D...text/html2009-04-20T18:20:06+01:00Cinly Ooi (co224@131.111.87.179)dcm2che
http://www.cambafx.org/wiki/programs/d/dcm2che?do=diff&1240248006
website: http://www.dcm2che.org It is a DICOM program suite INSTALLATION Make sure you define DCM2CHE_HOME environment variable to point to the top level of your unzipped copy of dcm2che. It is needed to construct the CLASSPATH for the java prog...text/html2008-07-09T19:29:36+01:00Cinly Ooi (co224@131.111.88.212)imgutils-image_format_convert
http://www.cambafx.org/wiki/programs/i/imgutils-image_format_convert?do=diff&1215628176
DEPRECATED It is still used for converting data between different data formats, and to break down files from 4D to 3Ds, and to construct 4D file from 3D files. If you have problems with very large Nifti4D files that you have to break down, try nii...text/html2008-07-09T19:28:25+01:00Cinly Ooi (co224@131.111.88.212)nii4dto3d.pl (in WBIC, not a CamBA program) - created
http://www.cambafx.org/wiki/programs/n/nii4dto3d.pl?do=diff&1215628105
This program can handle very large nifti 4d file. ...text/html2008-07-09T19:12:03+01:00Cinly Ooi (co224@131.111.88.212)extract_regional_statistics
http://www.cambafx.org/wiki/programs/e/extract_regional_statistics?do=diff&1215627123
The program is used to extract regional statistics data. General The output will give you statistics data from region 1 (0 if -Z used) up to and including the largest index in the region data file. This means if you only have one region, and it i...text/html2008-04-24T14:37:22+01:00Cinly Ooi (co224@131.111.88.212)Clustersignificancetest - created
http://www.cambafx.org/wiki/programs/c/clustersignificancetest?do=diff&1209044242
These section is only appropriate when the error occur in groupsetX.sh Error : Unable to open /path/to/tsafx/output/directory/MedianClusCrtVal.txt Check /path/to/tsafx/output/directory/Mediancambavoxellog.html. If it reports Errors: No values in ...text/html2008-04-07T13:32:38+01:00Cinly Ooi (co224@131.111.88.212)nifti_tool
http://www.cambafx.org/wiki/programs/n/nifti_tool?do=diff&1207571558
Effective version is nifticlib-0.2 Conversion between different NifTI file types When converting from one NifTI file type to another using -cbl, the program will only copy over header data imperfectly, i.e., the results does not duplicate the he...text/html2008-04-04T12:51:01+01:00Cinly Ooi (co224@131.111.88.212)niiactivation2png
http://www.cambafx.org/wiki/programs/n/niiactivation2png?do=diff&1207309861
This program attached activation to a base image and print it out as PNG file Activation Colour Schemes You can choose a particular colour scheme using –process-command <cmd> whose format is --process-command =<level>,<schem...text/html2008-04-01T18:57:28+01:00Cinly Ooi (co224@131.111.88.212)create-newtsafxlink.sh - created
http://www.cambafx.org/wiki/hosted/cambapowerpack/cdb/programs/c/create-newtsafxlink?do=diff&1207072648
create-newtsafxlink.sh create a subdirectory to host the analysis. It also copies data from previous analysis if requested. Data check list *.dm and *.nii file in the subject directory must not be broken symbolic link. If they are, they are not d...text/html2008-04-01T18:55:24+01:00Cinly Ooi (co224@131.111.88.212)CamBAdB Programs - created
http://www.cambafx.org/wiki/hosted/cambapowerpack/cdb/programs?do=diff&1207072524
Information about CamBA program. It is not a comprehensive list and is mainly used to document experience about individual programs, rather than how they are used. Included here are also third party programs used in CamBA DISCLAIMER Information i...text/html2008-04-01T18:52:47+01:00Cinly Ooi (co224@131.111.88.212)CamBA dataBase - created
http://www.cambafx.org/wiki/hosted/cambapowerpack/cdb?do=diff&1207072367
A set of add-on to CamBA designed to speed up data entry for large datasets. CamBAdB Programs ...text/html2008-04-01T18:51:49+01:00Cinly Ooi (co224@131.111.88.212)CamBA PowerPacks - created
http://www.cambafx.org/wiki/hosted/cambapowerpack?do=diff&1207072309
CamBA PowerPacks are a set of add-ons to CamBA which is designed to make CamBA easier to use. CamBA dataBase ...text/html2008-04-01T18:50:38+01:00Cinly Ooi (co224@131.111.88.212)Welcome to CamBAfx Wiki
http://www.cambafx.org/wiki/start?do=diff&1207072238
If you are looking for the homepage of CamBAfx, use the link below. http://www.cambafx.org CamBAfx website consists of the front page (above), this wiki and a shared blog with GenericFX. This is not a publicly editable wiki. Sections Please a...text/html2008-03-31T15:41:36+01:00Cinly Ooi (co224@131.111.88.212)MacOSX 10.5 (Leopard) specific issues
http://www.cambafx.org/wiki/camba/users/problems/os/macosx/leopard?do=diff&1206974496
If you check out from SVN only The libtoolize program to use is call /usr/bin/glibtool. Create a symbolic link from glibtool to libtool will do the trick. This is the preferred method. sudo ln -s /usr/bin/glibtoolize /usr/bin/libtoolize and typ...text/html2008-03-31T15:19:40+01:00Cinly Ooi (co224@131.111.88.212)User Section
http://www.cambafx.org/wiki/users?do=diff&1206973180
See also http://www.brainfx.org/wiki/users and http://www.genericfx.org/wiki/users Sections Start Up What to do if you have problems starting up CamBA Results HTML Output Standard Operating Procedures CamBA Useful Information (inc Tips ...