:orphan:

.. _ahelp_adjunct_apqc_tsnr_general:

*************************
adjunct_apqc_tsnr_general
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.. contents:: :local:


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OVERVIEW
========

.. code-block:: none

    
    Just an adjunct program for making TSNR plots for APQC.
    
    Ceci n'est pas un fichier d'aide utile!
    
    written by PA Taylor.
    

EXTRA OPTS
==========

.. code-block:: none

    
    -montgap        A
    -montcolor      A 
    -montx          A
    -monty          A
    -opacity        A
    -blowup         A
    -save_ftype     A
    -set_dicom_xyz  A B C
    -set_ijk        A B C
    -set_subbricks  A B C
    -olay_alpha     A
    -olay_boxed     A
    -thr_olay       A
    -ulay_range_nz  A B 
    -ulay_range     A B
    -delta_slices   A B C
    -olay_disc_hot_range  A B
    -olay_cont_max  A 
    -cbar_cont      A
    -no_cor
    -no_sag
    -no_axi
    -echo 
    

EXAMPLE
=======

.. code-block:: none

    
    1) case of having a mask (output will have discrete cbar, with ranges
       determined by percentiles within the mask):
    
        adjunct_apqc_tsnr                                 \
            -ulay         MNI152_2009_template_SSW.nii.gz \
            -focus        MNI152_2009_template_SSW.nii.gz \
            -olay         TSNR*HEAD                       \
            -mask         mask_epi_anat.*HEAD             \
            -prefix       img1                            \
            -prefix_cbar  img1.cbar
    
    2) case of NOT having a mask (output will have a continuous cbar, with
       ranges determined by percentiles within the whole volume):
    
        adjunct_apqc_tsnr                                 \
            -ulay         MNI152_2009_template_SSW.nii.gz \
            -focus        MNI152_2009_template_SSW.nii.gz \
            -olay         TSNR*HEAD                       \
            -prefix       img2                            \
            -prefix_cbar  img2.cbar
    
    3) case of using the discrete hot/cold color cbar, but user puts in
       the range for the colorbar (does not need/use mask):
    
        adjunct_apqc_tsnr                                 \
            -ulay         MNI152_2009_template_SSW.nii.gz \
            -focus        MNI152_2009_template_SSW.nii.gz \
            -olay         TSNR*HEAD                       \
            -olay_disc_hot_range  50 200                  \
            -prefix       img3                            \
            -prefix_cbar  img3.cbar
    
    4) case of using continuous cbar, and user puts in the range for it
       (does not need/use mask); you can also specify a continuous
       colorbar of choice here (not req):
    
        adjunct_apqc_tsnr                                 \
            -ulay         MNI152_2009_template_SSW.nii.gz \
            -focus        MNI152_2009_template_SSW.nii.gz \
            -olay         TSNR*HEAD                       \
            -olay_cont_max  200                           \
            -cbar_cont    Magma                           \
            -prefix       img4                            \
            -prefix_cbar  img4.cbar