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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Sep 15 2005 :  1:57:13 PM  Show Profile
The current version of the BXH tools has been tagged as 1.8.0 and installed on golgi (AIX) and \\gall\programs\BXH\bin (Win32). A list of changes between 1.7.0 and 1.8.0 follows. Note: several of the improvements had been installed piecemeal since the 1.7.0 release on March 28.
  • Many minor documentation and help message updates.
  • Many minor bug fixes and memory fixes.
  • Additional smarts added to dicom2bxh/bxhabsorb to add time and acquisition number (a.k.a. scan number) as a dimensions when appropriate.
  • Version 11 P-files are now supported by pfile2bxh /bxhabsorb.
  • bxh_event2table converts XML events files into tabular form, such as comma-separated values for use in Excel.
  • bxh_eventstats should apply queryfilter and queryepochexclude options correctly now.
  • bxh_eventstats now writes averages and standard deviations as percent of baseline, in addition to the unscaled numbers.
  • bxh_eventstats now supports frequency filtering (using the underlying program bxh_tfilter).
  • History entries added to the output of more tools.
  • Summary QA measures (shown at the top of the HTML page) are now also added to the XML events files.
  • New programs:
    • bxh_mean -- calculate the average of several input images
    • bxh_eventmerge -- merge values from events one XML events file into another. An event in any of the source files is merged into an event in the target file if the value of a given query matches.

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Sep 19 2005 :  4:38:20 PM  Show Profile
Version 1.8.1 of the tools has been installed on golgi, and is in the process of being installed in \\gall\programs\BXH\bin. This release mostly updates documentation/help messages, but also fixes a bug in bxh_eventstats. If your t-maps suddenly only had 1 timepoint when you expected them to have more, this update should fix it.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 04 2005 :  11:51:44 AM  Show Profile
Version 1.8.2 of the BXH tools has been installed on golgi and on BIAC Windows machines in \\gall\programs\BXH\bin. All updates other than documentation updates are minor, so should not affect you in any significant way.

Nearly all tools should now respond to the --help option which will give a detailed help message. Most tools will also respond to the --version option which will give the currently installed version of the tools.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 07 2005 :  3:20:10 PM  Show Profile
I neglected to perform a required update to gnuplot when updating the BXH tools to version 1.8.2. This has been fixed. If you have incomplete QA reports (missing plots/histograms), re-running the QA using bputil should fix it. QA reports created from Friday (Nov. 4) afternoon to Monday (Nov. 7) morning may be affected.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Dec 06 2005 :  4:24:23 PM  Show Profile
Version 1.8.3 of the BXH tools has been installed on golgi. This includes very minor updates, most for the BIRN. The following are the only changes you are likely to notice:
  • scan times recorded in the BXH files are more accurate for functional scans
  • pfile2bxh doesn't give a warning for Allen's newest pulse sequences
As always, please post if you notice any problems.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Feb 08 2006 :  2:57:13 PM  Show Profile
Version 1.8.4 of the BXH tools has been installed on golgi. This includes the following minor updates:
  • new options to bxh_eventstats (secsbefore/secsafter) which you probably won't use
  • updates to the time fields used in dicom2bxh for Siemens mosaic data
  • analyze2bxh now supports level 5 .mat files as written by newer versions of MATLAB and SPM
  • analyze2bxh now supports one-file (.nii) NIFTI files (two-file .hdr and .img already supported)
  • bxh2analyze now does not erase 4th dimension pixdim[] field even if writing out 3-D files
  • eprime2xml, presentation2xml, and eventstable2xml now support the $DURUNTIL and $DURUNTILNEXTROW magic values
  • pfile2bxh should now generate more reasonable orientation vectors for BIAC EPI data
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Mar 24 2006 :  12:00:45 PM  Show Profile
Version 1.8.5 of the BXH tools has been installed on golgi (AIX) and in \\gall\programs\BXH (Win32). This release includes mostly portability updates, and the following tool updates (many of which were already introduced as "previews" since the last release):
  • BXH files now include a <rasorigin> field for easy extraction of RAS origin coordinates. This is produced by any of the *2bxh or bxhabsorb tools
  • extensions to bxh_eventstats for Lihong
  • pfile2bxh now uses the "rotate" field in the per-slice table to generate correct bounding-box corners
  • showplay2xml now can generate XML events files from just a .ppf file
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jun 01 2006 :  5:28:04 PM  Show Profile
Version 1.8.6 of the BXH tools has been installed on golgi (AIX). In addition to minor bug fixes and code cleanup, the following modifications have been made:
  • Several tools now use "float" instead of "double" to conserve memory
  • compressed NIfTI-1 (usually with the prefix .nii.gz) is now a supported target for BXH files, and can now be created by bxhabsorb and analyze2bxh, and should be transparently supported for reading by all other command-line tools that read BXH files
  • bxh_eventstats now supports the --memorylimit option, which lets you restrict the amount of image data it should read at a time. This will enable you to run bxh_eventstats on higher-resolution images and also larger numbers of timepoints. For example, using "memorylimit 64" will restrict it to reading the input in 64MB blocks (the working space of which, of course, will be a few times greater than that as the program runs)
  • QA has been updated with several new items including masked versions of various metrics, and also plots of FWHM (smoothness) and outlier counts, courtesy of AFNI tools 3dFWHM and 3dToutcount
The previously installed version of tools is available in /usr/local/packages/xmlheader-1.8.5. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Edited by - syam.gadde on Jun 02 2006 10:26:02 AM
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jul 11 2006 :  10:52:05 AM  Show Profile
Version 1.8.7 of the BXH tools has been installed on golgi (AIX). The only modifications of interest are:
  • New --extracttrials option to bxh_eventstats
  • fmriqa_generate.pl (the program that generates QA reports) has been updated with many new options and cosmetic upgrades (including a navigation menu)
  • pfile2bxh updated for "epiduke" sequence
The previously installed version of tools is available in /usr/local/packages/xmlheader-1.8.6. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Edited by - syam.gadde on Jul 11 2006 11:21:21 AM
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jul 13 2006 :  12:04:57 PM  Show Profile
Version 1.8.7 of the tools has been installed on BIAC Windows machines in \\gall\programs\BXH\bin. See the above posts for a list of changes.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jul 31 2006 :  5:47:42 PM  Show Profile
Version 1.8.10 of the BXH tools has been installed on golgi (AIX). Updates include:
  • Fixes for reading version 5 .mat files (as written by later versions of MATLAB/SPM)
  • slice_duration in NIfTI-1 files is populated with a more appropriate value by bxh2analyze
  • pfile2bxh has updates for new pulse sequences and a fix for X/Y spacing for the epiduke sequence
  • showplay2xml will accept multiple blank lines between header and stimulus sections (though it is technically prohibited by the spec)
  • Various Win32 compilation fixes
The previously installed version of tools is available in /usr/local/packages/xmlheader-1.8.7. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Aug 09 2006 :  12:15:05 PM  Show Profile
Version 1.8.13 of the BXH tools has been installed on golgi (AIX). It will be installed on BIAC Windows machines (in \\gall\programs\BXH\bin) later this afternoon. Updates include:
  • More fixes for reading and writing .mat files by bxh2analyze, bxhabsorb, and analyze2bxh
  • other minor bug fixes
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.10 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.10. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Aug 14 2006 :  11:59:20 AM  Show Profile
Version 1.8.14 of the BXH tools has been installed on golgi (AIX) and BIAC Windows machines in \\gall\programs\BXH\bin.
  • showplay2xml fixes a timing extraction bug introduced in release 1.8.10 (July 31).
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.13 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.13. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Sep 22 2006 :  2:17:31 PM  Show Profile
Version 1.8.16 of the BXH tools has been installed on golgi (AIX), and will be soon installed on BIAC Windows machines in \\gall\programs\BXH\bin.
  • fmriqa_generate.pl adds help popups for each metric in the QA pages.
  • bxh_eventstats now supports FSL first-level analysis .feat directories as inputs using the --featinputs option, and in addition supports averaging or output in original functional, anatomical highres, or FSL standard space (using the --featavgspace or --featoutputspace options), and the averaging or output can be performed in a functional, highres, or FSL standard resolution/grid (using the --featavgrefvol or --featoutputrefvol options). Run bxh_eventstats --help for more details on the new options. For outputs using this new .feat functionality, the new tool bxh_eventstats_standardize will convert any number of eventstats outputs into standard space, optionally changing the resolution/grid (as above).
  • bxh_eventresp now supports a --reversemerge option to reverse the direction of the merge (i.e. fields are copied from the earlier "stimulus" event to the later "response" event, rather than the other way around).
  • pfile2bxh fixes a bug in storing dates/times on 64-bit machines (e.g. golgi)
  • showplay2xml now deals better with unexpected blank lines in the stimulus section of .ppf files
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.14 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.14. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Oct 05 2006 :  09:06:17 AM  Show Profile
Version 1.8.17 of the BXH tools has been installed on golgi (AIX), and on BIAC Windows machines in \\gall\programs\BXH\bin.
  • analyze2bxh and bxhabsorb updated to deal better with .mat files created on newer versions of MATLAB.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.16 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.16. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Oct 30 2006 :  3:49:19 PM  Show Profile
Version 1.8.19 of the BXH tools has been installed on golgi (AIX), and on BIAC Windows machines in \\gall\programs\BXH\bin.
  • dicom2bxh and bxhabsorb now support a --filename-sort option to deal with files whose fields do not provide enough information to sort the images. Also, the acqusition matrix is now read correctly for idiosyncratic files created by some scanners.
  • dicom2bxh and bxhabsorb now support BXH wrapping of .mgh and .mgz files, as created by FreeSurfer.
  • Calls to FSL's "flirt" program (used to apply FEAT-generated transforms) in bxh_eventstats are now moved to a helper function for use by multiple scripts
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.17 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.17. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
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