leej3
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afni_ci_test_data


			
			
				
					
						
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>HELP FILE FOR AP-QC</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>afni_proc.py's single subject QC report form</b></pre></div>
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>OVERVIEW</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>QC organization
    The quality control (QC) is organized into thematic blocks to
    check, such as original data acquisition, different alignments,
    motion, regression modeling, and more. At the top of the QC page,
    there is a navigation bar with a label for each QC block (vorig,
    ve2a, etc.) that functions as a button to the top of that section.

Rating
    Beneath each section label is a(n initially empty) QC button,
    which users can click to set a rating for that QC block and for
    the overall subject rating ("FINAL"). Clicking on the QC button
    toggles its state through good (+), bad (X) or other (?, which may
    include 'ugly', or just a hint to revisit later).  Users can also
    use convenient 'filler buttons' at the right (A+, Ax, etc.), when
    the ratings are constant/uniform-- one hopes for 'all good'
    processing, but who knows...

Commenting
    Additionally, users can ctrl+click on the QC button to enter a
    comment for that block.  For example, they can write why a rating
    was good or bad, or what question they have led them to rate it as
    'other'.

Saving
    Clicking SAVE will let the user save the QC ratings+comments on
    their computer for later use, such as inclusion/exclusion criteria
    for the subject in group analysis.  (NB: This action is treated
    the same as downloading a file from online, and is subject to
    standard limitations on simplicity due to browser security
    settings.)

See also
    The online web tutorial:
    https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/apqc_html/main_toc.html
    It's more verbose and pictorial, if that's useful.
</b></pre></div>
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>DEFINITIONS</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>QC block 
    One thematic section of the QC form (original data, alignment
    step, etc.).  Each block has a label in the navigation bar (vorig,
    ve2a, etc.)-- click on the label to jump to that block. Click on
    the button below the label to provide a rating for that block.

QC button
    Below each QC block label in the navigation bar is a button
    (initially empty after running afni_proc.py). The user can click
    on it to toggle its state to one of three ratings (good, +; bad,
    X; other, ?), as well as to enter a comment for that QC block (via
    ctrl+click).

'FINAL' 
    Label for the QC button to hold the user's overall/final
    evaluation of the subject's data and processing. (Clicking on this
    label does nothing.)

filler button 
    |A+|, |Ax|, |A?|-- located in the upper right corner of the
    navigation menu.  These can be used to provide uniform ratings
    across the QC buttons (click to fill empty buttons, double-click
    to fill *all* buttons, regardless of state).  
    |clr|-- double-clicking on this will empty all ratings+comments
    from the QC buttons.

'SAVE'
    Write the ratings+comments to disk.  This action is done through
    the browser, and is subject to the browser settings; probably
    users should not have the browser set to automatically download
    all files to the same location, for example.

'HELP'
    Button : well, how did you get here??

'BC', 'AC'
    When using the 'pythonic' HTML style, 1D-plotting (like motion
    enorm plots) also produces boxplots to summarize values.  When
    censoring has been applied, by default there will be two boxplots
    made: one of values 'before censoring' (BC), and one of values
    'after censoring' (AC).  Those labels are affixed in order to the
    titles of the boxplots.

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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>SET BUTTON RATING</b></center></pre></div>
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To record an evaluation, click the button below any section label, and
toggle through:
    + : good,
    X : bad,
    ? : other (or 'revisit').

For speed, you can click 'filler button' |A+| once to fill all *empty*
buttons with +, or doubly to fill *all* buttons with +.  |Ax| behaves
the same for X, and |A?| for ?.

Double-click |clr| to clear all rating and comment values.

Pro-tip: if data are mostly all in a single state like good or bad,
just use filler buttons to save yourself click time, and then just
click any individual buttons that are different.  </b></pre></div>
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>COMMENT</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>
Use ctrl+click on a QC button to open (or close) a comment window.  

Save a comment with the green (left) button, or hit Enter at any point.
Remove a comment with the pink (right) button, or hit Esc at any point.

Any QC button with a comment gets a pair of quotes added, like ''+''.
Comments are independent of rating, but adding a comment to an empty
button changes its rating to ''?'' (which can be altered further from
there).
</b></pre></div>
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>SAVE FORM</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>Click on the 'SAVE' button.  

Unfortunately, the file will not be directly saved by this, due to
security settings on most web-browsers, and the user will be prompted
to save the file as if downloading from the Web.</b></pre></div>
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>KEYBOARD NAVIGATION</b></center></pre></div>
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Use Tab to navigate the QC menu mirroring all above functionality.

Hit Tab to move through the menu.  Hit Enter on a section label to
scroll the page there.

On QC buttons hit Enter to toggle through the rating list.  Use
ctrl+Enter to open comments; as above, use Enter or Esc to keep or
erase, respectively.

On the filler buttons |A+|, |Ax| and |A?|, use Enter to fill empty
QC buttons and ctrl+Enter to fill *all* buttons. 
On |clr|, ctrl+Enter clears all rating and comment values.  
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<div  style="padding-top: 0px; margin-top: -0px;"><pre   class='padtop'  ><center><b>QC BLOCKS</b></center></pre></div>
<div  style="padding-top: 0px; margin-top: -0px;"  class='container'  ><pre><b>
vorig
    Volumetric mages of data (EPI and anat) in original/native space.
    *Coming soon*.
    
ve2a
    Volumetric images of the alignment of the subject's anat
    (underlay/grayscale) and EPI (overlay/hot color edges) volumes. Likely
    these will be shown in the template space, if using the tlrc block.
    
va2t
    Volumetric images of the alignment of the standard space template
    (underlay/grayscale) and subject's anat (overlay/hot color edges)
    volumes.
    
vstat
    Volumetric images of (full) F-stat of an overall regression
    model. These images are only created for task data sets, i.e., where
    GLTs or stimuli are specified (so not for resting state data).
    
mot
    Summary of motion and outlier information, which may each/both be
    used as censoring criteria.
    
    The 6 rigid body motion parameters (3 rotation + 3 translation) are
    combined into a single quantity: the Euclidean norm (enorm), which has
    approx. units of 'mm'.  Large changes in the enorm time series show
    moments of subject motion.
    
    Separate runs are shown with the background alternating between white
    and light gray.
    
    Boxplots summarize parameter values, both before censoring (BC) and
    after censoring (AC).
    
regr
    When processing with stimulus time series, both individual and
    combined stimulus plots are generated (with any censoring also shown).
    
    The degrees of freedom (DF) summary is also provided, so one can check
    if too many get used up during processing (careful with bandpassing!).
    
    And a grayplot of residuals is provided.
    
warns
    Several AFNI programs carry out consistency checks while
    processing (e.g., pre-steady state check, regression matrix corr
    warnings, left-right flip checks).  Warnings are conglomerated here.
    
    Each warning has one of the following levels:
         none undecided mild medium severe
    
    The warning level is written, with color coding, at the top of each
    warning's text box.  The QC block label 'warns' at the top of the page
    is also colored according to the maximum warning level present.  
    
radcor
    @radial_correlate plots (per run, per block). These can show
    scanner coil artifacts, as well as large subject motion; both factors
    can lead to large areas of very high correlation, which would be
    highlighted here.  
    
qsumm
    This is the output of @ss_review_basic, which contains a loooot of
    useful information about your single subject processing.
    </b></pre></div></body></html>