1NIPY_DIAGNOSE(1)                 User Commands                NIPY_DIAGNOSE(1)
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NAME

6       nipy_diagnose – Calculate and write results for diagnostic screen
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SYNOPSIS

9       nipy_diagnose      [-h]      [--out-path OUT_PATH]     [--out-fname-la‐
10       bel OUT_FNAME_LABEL]                        [--ncomponents NCOMPONENTS]
11       [--time-axis TIME_AXIS] [--slice-axis SLICE_AXIS] filename
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DESCRIPTION

14       nipy_diagnose(1)  will  generate a series of diagnostic images for a 4D
15       fMRI image volume.  The following images will be generated.   <ext>  is
16       the input filename extension (e.g. ‘.nii’):
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18              • components_<label>.png : plots of PCA basis vectors
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20              • max_<label><ext> : max image
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22              • mean_<label><ext> : mean image
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24              • min_<label><ext> : min image
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26              • pca_<label><ext> : 4D image of PCA component images
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28              • pcnt_var_<label>.png :  percent  variance  scree  plot for PCA
29                components
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31              • std_<label><ext> : standard deviation image
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33              • tsdiff_<label>.png : time series diagnostic plot
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35       The filenames for the outputs are  of  the  form  <out-path>/<some_pre‐
36       fix><label><file-ext>  where  <out-path>  is  the path specified by the
37       --out-path option, or the path of the input filename; <some_prefix> are
38       the standard prefixes above, <label> is given by --out-label, or by the
39       filename of the input image (with  path  and  extension  removed),  and
40       <file-ext>  is ‘.png’ for graphics, or the extension of the input file‐
41       name for volume images.  For example, specifying only the  input  file‐
42       name   /some/path/fname.img   will   generate  filenames  of  the  form
43       /some/path/components_fname.png, /some/path/max_fname.img etc.
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OPTIONS

46   POSITIONAL ARGUMENTS
47       filename
48              4D image filename
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50   OPTIONAL ARGUMENTS
51       -h, --help
52              Show a help message and exit
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54       --out-path OUT_PATH
55              Path for output image files
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57       --out-fname-label OUT_FNAME_LABEL
58              Mid part of output image filenames
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60       --ncomponents NCOMPONENTS
61              Number of PCA components to write
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63       --time-axis TIME_AXIS
64              Image axis for time
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66       --slice-axis TSLICE_AXIS
67              Image axis for slice
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SEE ALSO

70       nipy_3dto4d(1), nipy_4d_realign(1), nipy_4dto3d(1), nipy_tsdiffana(1)
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74                                 February 2023                NIPY_DIAGNOSE(1)
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