adjunct_apqc_tsnr_general

OVERVIEW

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

-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

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