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processing_stream_-_quality_assessment [2010/05/27 06:08]
jochen created
processing_stream_-_quality_assessment [2010/10/26 21:26] (current)
jochen created
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 ===== 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:
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 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 optionsplease 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(sor 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. 
processing_stream_-_quality_assessment.txt · Last modified: 2010/10/26 21:26 by jochen