fmriquality
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fmriquality [2010/06/17 14:18] – created jochen | fmriquality [2010/06/17 19:09] – integrated the information in the QA page jochen | ||
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===== Requirements ===== | ===== Requirements ===== | ||
- | To run the fMRI quality checking function, the images need to be in one of the functional imaging data formats currently supported by the xff class (Analyze/NIftI, FMR/STC, VTC). | + | To run the fMRI quality checking function, the images need to be in one of the functional imaging data formats currently supported by the xff class: |
+ | * BrainVoyager' | ||
+ | * BrainVoyager' | ||
+ | * SPM' | ||
===== Function reference ('help fmriquality' | ===== Function reference ('help fmriquality' | ||
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===== Usage ===== | ===== Usage ===== | ||
The most basic (and pre-configured) way of running fmriquality is by simply passing in the filename(s) or object of the run to check: | The most basic (and pre-configured) way of running fmriquality is by simply passing in the filename(s) or object of the run to check: | ||
- | * using Analyze files: <code matlab fmriquality_example1.m> | + | * using Analyze files: <code matlab fmriquality_example1.m> |
* using a BrainVoyager QX FMR file: <code matlab fmriquality_example2.m> | * using a BrainVoyager QX FMR file: <code matlab fmriquality_example2.m> | ||
qas = fmriquality(fmr);</ | qas = fmriquality(fmr);</ | ||
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% running fmriquality | % running fmriquality | ||
fmriquality(qafiles, | fmriquality(qafiles, | ||
+ | * create a quality assessment struct for all VTCs in an MDM, applying robust temporal filtering: <code matlab fmriquality_example4.m> | ||
+ | for study = 1: | ||
+ | | ||
+ | % perform quality assessment | ||
+ | q = fmriquality(mdm.XTC_RTC{study, | ||
+ | | ||
+ | % store as VTCNAME_qasheet.mat | ||
+ | save([mdm.XTC_RTC{study, | ||
+ | end</ | ||
+ | |||
+ | In case the QA sheet is not shown by the function (flag '' | ||
+ | |||
+ | <code matlab fmriqasheet_example.m> | ||
+ | load CPU4212_run3_qasheet.mat | ||
+ | |||
+ | % open QA sheet | ||
+ | fmriqasheet(q);</ | ||
+ | |||
If the '' | If the '' | ||
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When passed to [[fmriqasheet]], | When passed to [[fmriqasheet]], | ||
+ | |||
+ | ==== Usage notes ==== | ||
+ | Please be aware that the first argument **must** be a list of filenames; so, even for a single NIftI ([[xff - NII format|NII]]) file, a cell array must be passed in: | ||
+ | |||
+ | <code matlab fmriquality_example5.m> | ||
+ | qas = fmriquality({' | ||
+ | |||
+ | Also, please note that motion parameter estimation requires between one and several minutes (depending of the length of the run and whether or not robust motion estimation is employed). The **runtime also easily increases tenfold when robust temporal filtering is used**. In other words, these options are more useful and meant for situations where the fmriquality function is part of a larger script that automatically checks the quality of all incoming data instead of being used from the command line in a more interactive way! | ||
+ | |||
+ | Finally, at the moment, the " |
fmriquality.txt · Last modified: 2010/11/26 18:50 by jochen