7.1.430. gen_epi_review.py

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This program will generate an AFNI processing script that can be used to review EPI data (possibly called @review_epi_data).

The @review_epi_data script is meant to provide an easy way to quickly review the (preferably un-altered) EPI data. It runs afni and then a looping set of drive_afni commands.

Note that there should not be another instance of ‘afni’ running on the system when the script is run, as ‘drive_afni’ will communicate with only the first invoked ‘afni’ program.

The most simple usage comes with the -dsets option, along with the necessary pieces of the gen_epi_review.py command.

These examples assume the EPI dataset names produced as a result of the afni_proc.py processing script proc.sb23.blk, produced by the command in AFNI_data4/s1.afni_proc.block, provided with the class data.

Yes, that means running the s1.afni_proc.block (tcsh) script to call the afni_proc.py (python) script to produce the proc.sb23.blk (tcsh) script, which calls the gen_epi_review.py (python) script to produce the @review_epi_data (tcsh) script, which can be run to review your EPI data. Ahhhhhhh... :)

Note that when using wildcards, the datasets must exist in the current directory. But when using the {1,2,..} format, the files do not yet need to exist. So command #2 could be run anywhere and still create the same script, no data needed.

  1. simple usage, just providing datasets (and general options)

    gen_epi_review.py -dsets pb00.sb23.blk.r??.tcat+orig.HEAD

  2. expand 5 runs with shell notation, rather than wildcards, and specify an alternate script name

    gen_epi_review.py -dsets pb00.sb23.blk.r{1,2,3,4,5}.tcat

-script @review_epi_5runs
  1. choose to see all three image windows

    gen_epi_review.py -dsets pb00.sb23.blk.r*.tcat+orig.HEAD

-windows sagittal axial coronal -script @review_epi_windows
  1. specify the graph size and position (can do the same for image windows)

    gen_epi_review.py -dsets pb00.sb23.blk.r*.tcat+orig.HEAD

-gr_size 600 450 -gr_xoff 100 -gr_yoff 200 -script @review_epi_posn

OPTIONS:

informational arguments:

-help : display this help
-hist : display the modification history
-show_valid_opts : display all valid options (short format)
-ver : display the version number

-dsets dset1 dset2 ... : specify input datasets for processing

e.g. -dsets epi_r*+orig.HEAD

This option is used to provide a list of datasets to be processed in the resulting script.

-script SCRIPT_NAME : specify the name of the generated script

e.g. -script review.epi.subj23

By default, the script name will be ‘@’ followed by the name used for the ‘-generate’ option. So when using ‘-generate review_epi_data’, the default script name will be '@review_epi_data‘.

This ‘-script’ option can be used to override the default.

-verb LEVEL : specify a verbosity level

e.g. -verb 3

Use this option to print extra information to the screen

-windows WIN1 WIN2 ... : specify the image windows to open

e.g. -windows sagittal axial

By default, the script will open 2 image windows (sagittal and axial). This option can be used to specify exactly which windows get opened, and in which order.

Acceptable window names are: sagittal, axial, coronal

-im_size dimX dimY : set image dimensions, in pixels

e.g. -im_size 300 300

Use this option to alter the size of the image windows. This option takes 2 parameters, the pixels in the X and Y directions.

-im_xoff XOFFSET : set the X-offset for the image, in pixels

e.g. -im_xoff 420

Use this option to alter the placement of images along the x-axis. Note that the x-axis is across the screen, from left to right.

-im_yoff YOFFSET : set the Y-offset for the image, in pixels

e.g. -im_xoff 400

Use this option to alter the placement of images along the y-axis. Note that the y-axis is down the screen, from top to bottom.

-gr_size dimX dimY : set graph dimensions, in pixels

e.g. -gr_size 400 300

Use this option to alter the size of the graph window. This option takes 2 parameters, the pixels in the X and Y directions.

-gr_xoff XOFFSET : set the X-offset for the graph, in pixels

e.g. -gr_xoff 0

Use this option to alter the placement of the graph along the x-axis. Note that the x-axis is across the screen, from left to right.

-gr_yoff YOFFSET : set the Y-offset for the graph, in pixels

e.g. -gr_xoff 400

Use this option to alter the placement of the graph along the y-axis. Note that the y-axis is down the screen, from top to bottom.

  • R Reynolds June 27, 2008

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