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.. _ahelp_desphinxify:

***********
desphinxify
***********

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Overview
========

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    This is a simple program that *might* be useful for desphinxifying
    datasets. That is, when datasets are acquired in "sphinx" position,
    this will try to reorient them to match with axial/coronal/sagittal
    definitions standard to human neuroimaging. This may be useful
    particularly when processing nonhuman datasets
    
    Importantly, this program really only reliable **if** the user knows
    the correct final dataset orientation, to verify. We can recommend a
    useful intermediate orientation to reorient the data correctly, but
    the user is in charge of being user.
    
    ver  = 0.0
    auth = PA Taylor (SSCC, NIMH, NIH)
    

Options
=======

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    -input II         :(req) input dset name
    
    -prefix PP        :(req) output dset name (can include path)
    
    -orient_mid OM    :(req) intermediate orientation value, which determines
                       how the input dataset is effectively rotated (from
                       RAI orientation) in order to desphinxify it.  
                       **NB:** a commonly used value here is: RIP.  
                       However, users must verify this, particularly to get
                       left and right correct (other mistakes in orientation
                       tend to be more visually apparent). That is why there is
                       no default value: please check this with a pilot dataset
                       for your study.
    
    -workdir WD      : working directory name (just name, no path;
                       will be subdirectory of the output location)
    
    -overwrite       : when writing output, overwrite any preexisting
                       dataset (def: do not overwrite)
    
    -no_clean        : when done, do not remove temporary working
                       directory (def: do remove woroking directory
    
    -echo            : run very verbosely (with 'set echo' on)
    
    -ver             : display program version
    
    -help            : show help
    
    -hview           : show help in text editor
    
    

Examples
========

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    1) Basic usage:
    
         desphinxify                                \
            -orient_mid  RIP                        \
            -input       sub-001_T1w.nii.gz         \
            -prefix      sub-001_T1w_DSPH.nii.gz
    
       ... and verify/validate results, for a given collection protocol.