:orphan: .. _ahelp_gen_epi_review.py: ***************** gen_epi_review.py ***************** .. contents:: :local: | .. code-block:: none =========================================================================== 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. -------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------- 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. ---------------------------------------- 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 ---------------------------------------- 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 ===========================================================================