This shows you the differences between two versions of the page.
processing_stream_-_quality_assessment [2010/05/27 06:08] jochen created |
processing_stream_-_quality_assessment [2010/10/26 21:26] jochen created |
||
---|---|---|---|
Line 2: | Line 2: | ||
===== Motivation ===== | ===== Motivation ===== | ||
- | There are several things that can go wrong during the acquisition phase (scanning) of a subject. Among those are several that impact the usability of a subject's dataset. While any given project is still in the stage of data collection (subjects are still being scanned), there is always the chance to decide that a particular subject might introduce too much noise into the eventually performed group statistic and should be discarded (and in this case replaced by another subject). | + | There are several things that can go wrong during the acquisition phase (scanning) of a subject, some of which severely impact the usability of a subject's dataset. While any given project (study) is still in the stage of data collection (subjects are still being scanned), there is always the chance to decide that a particular subject might introduce too much noise into the eventually performed group statistic and should be discarded (and in this case replaced by another subject). |
Relevant for that decision could be one of the following issues: | Relevant for that decision could be one of the following issues: | ||
Line 14: | Line 14: | ||
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 (Analyze/NIftI, FMR/STC, VTC). | ||
- | ===== Usage ===== | + | ===== Steps ===== |
- | For additional options, please consult the [[fmriquality|fmriquality reference]] manual page. | + | The assessment is divided into two separate steps: one that performs several computational analysis and stores several results in a structure (which can be saved to disk for later), and a second step that assumes user interaction (i.e. manual inspection of the actual results of the computations). |
- | 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: | + | ==== Computation step (fmriquality) ==== |
- | <code matlab>% using Analyze files | + | Please consult the [[fmriquality|fmriquality reference]] manual page for all options and outputs. |
- | qas = fmriquality(findfiles(sessionfolder, '*.img')); | + | |
- | % alternatively, for FMR | + | ==== Assessment step (fmriqasheet) ==== |
- | fmr = xff('*.fmr', 'Select FMR for which you want to check the data quality...'); | + | The output of [[fmriquality]] can be passed on to [[fmriqasheet]], which in turn creates a new figure and displays part of the information in the structure, which can be used to decide on whether or not a subject would likely introduce too much noise/bias at the group level. |
- | qas = fmriquality(fmr);</code> | + | |
- | The returned variable is of type struct and contains at least the following fields: | ||
- | <file> .Dims 1x4 array, size | ||
- | .Filename the first filename given | ||
- | .Masks automatically detected masks (foreground, background, etc) | ||
- | .Raw mean, stdev, and null-voxel image | ||
- | .TempFiltered re-created summary values/maps after applying temporal filtering | ||
- | .Quality summary images trying to capture overall quality measures (SNR, CNR, etc.) | ||
- | .TC diverse time courses</file> | ||
- | |||
- | The output of [[fmriquality]] can be passed on to [[fmriqasheet]], which in turn creates a new figure and displays part of the information in the structure, which can be used to decide on whether or not a subject would likely introduce too much noise/bias at the group level. |