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jimmy.dias
BIAC Alum

USA
210 Posts
Posted - Oct 05 2004 :  09:05:07 AM  Show Profile  Visit jimmy.dias's Homepage  Reply with Quote
Hi all,

SPM99 Motion Correction using bputil now does by default registration across all runs within a series to the first image of the first run instead of within-run registration.

A major bug fix for the SPM99 Smoothing function within bputil has also been deployed. The problem was that instead of using a fixed kernel size, the smoothing function used a loop index for the kernel size instead of a static default kernel size or one specified by the user. This has been an undiscovered bug that dates back to November 2003.

Both fixes have been made to the following scripts that bputil uses under the covers (i.e. motioncorrect and smooth).

motioncorrect
smooth

bputil Updates that allow users to select which runs to process are on the way.

Jimmy

evan.gordon
BIAC Alum

12 Posts
Posted - Nov 02 2004 :  1:52:49 PM  Show Profile  Reply with Quote
I noticed that while the motion-corrected images are now registered to the first image of the first run, the realignment parameters listed in the "realignment_params_aV0001.txt" file for each run are still based on within-run registration. Is there any way to make this text file reflect the true realignment parameters used by the program?

Also, I was wondering if it is possible to make bputil spit out headers (bxh or otherwise) for each individual image file generated, so that individual timepoints can be seperately loaded by readmr. This would be very useful in experiments where the runs are long enough that matlab has trouble holding an entire run in memory.

Thanks,
Evan
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charles.michelich
BIAC Alum

USA
183 Posts
Posted - Nov 02 2004 :  2:06:13 PM  Show Profile  Reply with Quote
Evan,

You do not need a separate BXH header for each file in order to read a portion of the data specified by a BXH file. readmr is capable of doing this using the "dataselect" argument. For instance, to read the 18th time point of the file "example.bxh", type the following:
img = readmr('example.bxh', 'BXH', {'','','',18});
Or to read the 12th through the 25th time points in the same file, type:
img = readmr('example.bxh', 'BXH', {'','','',12:25});
See help readmr for more details.

You can also load a subset of the data using the readmr GUI. Just specify the subset of the data you want to read in the "Selector" fields. If you leave a selector blank, readmr will read all of the data in that dimension.

Chuck
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petty
BIAC Staff

USA
453 Posts
Posted - Nov 02 2004 :  2:06:46 PM  Show Profile  Reply with Quote
many of the analysis/pre-processing scripts look for the only bxh in the data folders so it may not be a good idea to have a bxh for every image. however you can read in individual images via their header (.hdr) file, or you can pull out certain timepoints through matlab (ie: func=readmr(data,(:,:,:,10:25));
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petty
BIAC Staff

USA
453 Posts
Posted - Nov 02 2004 :  2:07:46 PM  Show Profile  Reply with Quote
chuck hit submit before me ... you got me this time by 30 seconds
Edited by - petty on Nov 02 2004 2:08:28 PM
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