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gen_epi_review.py:
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.
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examples:
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
3. 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
4. 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
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OPTIONS:
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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
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required argument:
-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.
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optional arguments:
-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
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geometry arguments (optional):
-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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