Duke-UNC Brain Imaging and Analysis Center
BIAC Forums | Profile | Register | Active Topics | Members | Search | FAQ
Username:
 Password:
Save Password   Forgot your Password?
 All Forums
 Support Forums
 BXH Header Support
 BXH tools version 1.8.0		  New Topic  Topic Locked
 Printer Friendly
Previous Page
Author Previous Topic Topic Next Topic
Page: of 2

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 01 2006 :  3:40:51 PM  Show Profile
Version 1.8.20 of the BXH tools has been installed on golgi (AIX), and on BIAC Windows machines in \\gall\programs\BXH\bin.
  • dicom2bxh and bxhabsorb fix a memory bug introduced in 1.8.19.
  • pfile2bxh and bxhabsorb support the new --usemrorigin to force the origin to be read from the MR structure rather than the slice table.
  • bxh2analyze supports the new --zeroorigin option to force the origin in output .hdr, .nii., and .mat files to be 0,0,0 (may be useful if you want to tell SPM that the origin is "unspecified")
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.19 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.19. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 02 2006 :  10:08:02 AM  Show Profile
Version 1.8.21 of the BXH tools has been installed on golgi (AIX).
  • bxh_eventresp now actually respects the --maxresptime option
  • bxh2analyze supports the new --preferanalyzetypes option; this tells it to use Analyze 7.5 data types when possible (i.e. no under/overflow) when writing SPM or NIfTI-1 files.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.20. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 16 2006 :  12:33:16 PM  Show Profile
Version 1.8.22 of the BXH tools has been installed on golgi (AIX).
  • bxhselect and fmriqa_count now work with 3-D data and data not in xyzt order.
  • fmriqa_generate.pl fixes a mislabeling in the masked/detrended center of mass (Z) plots.
  • pfile2bxh uses a new way to calculate bounding box corners for 4T epiduke data.
  • showplay2xml fixes codenames/codetable support.
  • bxh2analyze and all other tools now respect the "rasorigin" field on input.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.21. 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 Nov 16 2006 12:35:50 PM
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Feb 05 2007 :  4:38:30 PM  Show Profile
Version 1.8.29 of the BXH tools has been installed on golgi (AIX), in \\gall\programs\BXH\bin (Windows) and packages have also been created for Linux (contact me). Updates since version 1.8.22 include:
  • fmriqa_phantomqa.pl introduces new QA measures (ghostiness (for EPI data), spatial FWHM (sometimes interpreted as "smoothness"), etc.), and improvements to existing QA measures (provided by fmriqa_phantomqa)
  • mgh2bxh now writes a "compression" field into the .bxh file to indicate that the wrapped .mgz file is compressed with gzip. Also fixes to height and width calculation.
  • bxh_binop now properly supports the --scalar option.
  • Some updates to dicom2bxh to deal with DICOM fields with unusual values in particular fields. Also, excessively long argument lists are truncated in the saved history.
  • analyze2bxh now should extract the t-dimension spacing from NIfTI-1 files in the correct units.
  • bxh2analyze supports writing to single-file NIfTI-1 (.nii) with the new --nii option.
  • bxh_eventstats now supports the --tcomparesummary option (where each trial is "summarized" by a smaller number of points before performing t-comparisons).
  • bxh_eventstats can now run on .feat directories that don't have any of the highres/func/standard brains that are not explicitly required by the given options.
  • bxh_mean fixes a bug when using --dimension dataset (before the bug fix, only the first input file was used).
  • New utilities: bxh_concat and bxh_unop
  • New utilities: several aliases for *2bxh programs for creating XCEDE files (in *2xcede programs, the --xcede option is implicit).
  • New utilities: xcede_test_query.pl is a simple way to test eventstats queries on the command-line without an options file. xcede_extract_schedules.pl is the more soberly-named equivalent to a script FIPS-ExtractSchedulesAux.pl that some people are using to create FSL stimulus schedule files from XML events files using queries.
  • several minor memory fixes
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.22 and on BIAC windows machines in \\gall\programs\BXH\bin_1.8.20. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Apr 18 2007 :  3:42:07 PM  Show Profile
Version 1.8.38 of the BXH tools has been installed on golgi (AIX), and packages have also been created for Linux (contact me). Updates since version 1.8.29 include:
  • dicom2bxh normalizes time datapoints to start at 0 for Siemens DICOM. Also fix an error reading past Siemens DICOM text header.
  • mgh2bxh now writes a "compression" field into the .bxh file to indicate that the wrapped .mgz file is compressed with gzip. Also fixes to height and width calculation.
  • afni2bxh deals better with missing fields.
  • analyze2bxh reads updated matrix in SPM2 (and later) .mat files.
  • bxh2analyze puts the right magic number in single-file nifti-1 images (--nii option).
  • bxh_eventstats now allows an arbitrary reference volume, and now writes out percent-signal-change summaries. Masks now applied to correlations.
  • bxh_unop can use the NIFTI statistics library to calculate statistics from the input images.
  • New program bxh_eventstats_combine to combine the results of several eventstats runs.
  • several other fixes and additional functionality
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.29. 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 Apr 18 2007 3:42:52 PM
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - May 15 2007 :  11:02:09 AM  Show Profile
Version 1.8.40 of the BXH tools has been installed on golgi (AIX), and packages have also been created for Linux (contact me). Updates since version 1.8.38 include:
  • fmriq_minmax now gives a warning if it finds non-finite values in the data (like NaN, Infinity, etc.).
  • dicom2bxh/dicom2xcede fixes a header reading problem with Siemens private headers.
  • bxh_applymask/bxh_binop fix a bug that occurs when one of the inputs needs to be replicated to match the size of the other, and if that input is not a 32-bit float or integer type.
  • bxh_epochavg now sets the standard deviation to 0 for values of N equal to 0 and (now) 1.
  • bxh_eventstats now prohibits underscores in query labels (underscores are used to separate important fields in output file names).
  • bxh_eventstats_combine fixes a bug where extra copies of "n", "avg", and "std" images in summaries were combined.
  • bxh_eventstats_combine supports a --maxprocs option for simple parallelization (though since it is mostly disk bound, --maxprocs=2 is likely to give the maximum benefit, if any).
  • bxh_ttest no longer writes NaNs for any voxel and instead acts as if those voxels were masked.
  • eprime2xml/presentation2xml/eventstable2xml supports "deci-milliseconds" (dmsec) as a units type (as used by Presentation) and DURUNTILNEXTROW works even on events occuring in the last row.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.38. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - May 21 2007 :  1:07:28 PM  Show Profile
Version 1.8.41 of the BXH tools has been installed on golgi (AIX), and packages have also been created for Linux (contact me). Updates since version 1.8.40 include:
  • eprime2xml fixes a bug introduced in the last release.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.40. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jul 02 2007 :  2:29:05 PM  Show Profile
Version 1.8.42 of the BXH tools has been installed on golgi (AIX), Windows BIAC machines (in \\gall\programs), and packages have also been created for Linux (contact me). Updates since version 1.8.41 include:
  • fmriqa_generate.pl now supports a --forcetr option. It also fixes a bug where the masked center-of-mass plot in the Z direction was not being displayed. Some images are now intelligently auto-scaled/windowed for display so extreme outliers do not affect min/max values in colormap.
  • Minor fix to allow bare-bones prefix files in bxh_eventstats_combine
  • xcede_extract_schedules.pl now gives a warning message for incorrectly-quoted lines in the query file (rather than hanging indefinitely)
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.41 and on BIAC Windows machines in \\gall\programs\BXH\bin_1.8.29 . Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jul 16 2007 :  3:02:34 PM  Show Profile
Version 1.8.43 of the BXH tools has been installed on golgi (AIX), and packages have also been created for Linux (contact me). Updates since version 1.8.42 include:
  • fmriqa_generate.pl fixes a bug where the count of masked running difference volumes greater than the first (default 1% of mean) threshold was not being calculated correctly.
  • bxh_eventstats_combine now should combine tmaps one-at-a-time (rather than all simultaneously). Will now also warn you if you specify a group name (in --groupcompare) that doesn't exist in the prefix file.
  • dicom2bxh supports storing multiple TE values from difference images from Siemens scanners. EffectiveEchoSpacing is extracted from GE DICOM images.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.42. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Sep 12 2007 :  12:14:40 PM  Show Profile
Version 1.8.45 of the BXH tools has been installed on golgi (AIX), and packages have also been created for Linux (contact me). Updates since version 1.8.43 include:
  • dicom2bxh: Fix Mosaic interpretation of dReadoutFOV and dPhaseFOV.
  • analyze2bxh: fix memory error.
  • bxh2analyze: Fix issue where non-time 4th (and higher) dimensions were resulting in a 4th dimension size of 0 for -v (4-D output).
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.43. Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 09 2007 :  12:23:58 PM  Show Profile
Version 1.8.50 of the BXH tools has been installed on golgi (AIX), \\gall\programs\BXH (Win32), and packages have also been created for Linux (contact me). Updates since version 1.8.45 include:
  • Style changes to fmriqa_generate.pl output. FWHM metrics added to output XML file. fmriqa_spikiness now ignores voxels that are unchanging across the time series.
  • dicom2bxh and pfile2bxh add some "sense"-specific fields.
  • pfile2bxh includes some orientation fixes.
  • New tool 3column2xml to convert (FSL-compatible) 3-column timing files to event XML files.
  • analyze2bxh: change default origin from 0,0,0 to (negative) half FOV.
  • bxh2analyze: new --niigz option writes compressed NIfTI-1 directly. Origin values for non-axial scans now set correctly.
  • bxh_eventstats: updates for FSL 4.0 and some more sanity checks.
  • bxh_eventstats_combine now explicitly requires brainmask in all inputs, and exits if it doesn't exist.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.45 and on gall in \\gall\programs\BXH\bin_1.8.45 . Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Apr 04 2008 :  2:04:43 PM  Show Profile
Version 1.8.59 of the BXH tools has been installed on golgi (AIX), \\gall\programs\BXH (Win32), and packages have also been created for Linux: Updates since version 1.8.50 include:
  • fmriqa_generate.pl supports the --timeselect option. Also now writes a log file of all command-lines it runs. Better auto-scaling of images to exclude extreme outliers from scaled min/max.
  • dicom2bxh, bxhabsorb extracts more info from DICOM files (all fields in the MR Image Module). GE diffusion directions are read directly from the header, rather than a hardcoded table.
  • bxh_eventstats now writes BXH-wrapped compressed NIFTI images (rather than raw .img files). Trial summary data is now transformed to output space as it should have already. Add single-condition t-tests (output images are _zerotmap).
  • Various tools: Binary data files that happen to look like gzip-compressed data (but aren't) should now be read correctly.
  • Various tools: BXH files wrapping a single 3-D mosaic file (from Siemens DICOM now should read correctly.
  • Preliminary support for XCEDE 2.
  • New tool bxh_transform allows you to apply an FSL-style transformation matrix to a BXH/XCEDE image.
  • pfile2bxh now uses the nframes field to figure out time points if there is no sequence-specific info.
The previously installed version of tools is available on golgi in /usr/local/packages/xmlheader-1.8.50 and on gall in \\gall\programs\BXH\bin_1.8.50 . Any problems or questions should be addressed to the "Analysis Software Support" forum (http://www.biac.duke.edu/forums/forum.asp?FORUM_ID=7).
Go to Top of Page
Page: of 2 Previous Topic Topic Next Topic  
Previous Page
 New Topic  Topic Locked
 Printer Friendly
Jump To:
BIAC Forums © 2000-2010 Brain Imaging and Analysis Center Go To Top Of Page
This page was generated in 0.3 seconds. Snitz Forums 2000