:orphan: .. _ahelp_@djunct_4d_imager: ***************** @djunct_4d_imager ***************** .. contents:: :local: | .. code-block:: none # ------------------------------------------------------------------------ The program is useful for viewing the same slice across the 'time' dimension of a 4D data set. It is used in several of FATCAT's fat_proc* functions (e.g., viewing DWIs). But because it seemed so useful, it now has some basic help for basic usage by *expert* AFNI users! The program outputs the following in sets of three, one for each spatial axis: + an image of the same central slice across volumes along the time axis, with the brightness range constant across volume ("*onescl*" images); that is, the same grayscale in each panel corresponds to the same numerical value. + an image of the same central slice across volumes along the time axis, with the brightness range possibly *varying* for each panel across volume ("*sepscl*" images); that is, the grayscale value in each panel can (and likely will) correspond to *a different* numerical value. Useful, for example, for checking details in DWIs, where the expected scale of values can change dramatically across volumes. + (with option flag) a movie version of the "onescl" images, showing one slice at a time. + (with option flag) a movie version of the "sepscl" images, showing one slice at a time. The panel dimensionality in each of the above montage images is calculated to be approximately golden ratio-ish. (with blank panels appended as deemed desirable; blank slices are *not* appended to the dset, they are just added for the montage visualization). Slice numbers are shown in both the image panels and the movie panels. This program is a very basic wrapper around @chauffeur_afni. It is useful as a quality control (QC) generator, driving AFNI functionality to make images *and* movies of a data set while processing (working in a virtual X11 environment using xvfb, so that this generates images/movies even on a remote terminal). written by PA Taylor (NIMH, NIH, USA). # ======================================================================== -help, -h :see helpfile (here!) -ver :see version number -inset UUU :ulay dset (required). Probably 4D (hence the name of this program...). -prefix PPP :prefix for output files (required). -do_movie MTYPE :specify type of movie file. Basically, one of two options: MPEG AGIF This is optional; by default, a montage of PNG images is created: the same slice across the 4D set. -no_clean :by default, the temporary directory made by this program is deleted when finishing. Use this option to keep the final intermediate files. # ======================================================================== EXAMPLE: # 1) Um, just view all the volumes in a DWI acquisition, both as a # montage saved as a PNG file and as an mpeg file. @djunct_4d_imager \ -inset MY_DWIs.nii.gz \ -prefix PRETTY_DWIS \ -do_movie AGIF