AFNI program: Ifile
Output of -help
Usage: Ifile [Options] <File List>
[-nt]: Do not use time stamp to identify complete scans.
Complete scans are identified from 'User Variable 17'
in the image header.
[-sp Pattern]: Slice acquisition pattern.
Sets the slice acquisition pattern.
The default option is alt+z.
See to3d -help for acceptable options.
[-od Output_Directory]: Set the output directory in @RenamePanga.
The default is afni .
<File List>: Strings of wildcards defining series of
GE-Real Time (GERT) images to be assembled
as an afni brick. Example:
or Ifile '083/I.*' '103/I.*' '123/I.*' '143/I.*'
The program attempts to identify complete scans from the list
of images supplied on command line and generates the commands
necessary to turn them into AFNI bricks using the script @RenamePanga.
If at least one complete scan is identified, a script file named GERT_Reco
is created and executing it creates the afni bricks placed in the afni directory.
How does it work?
With the -nt option: Ifile uses the variable 'User Variable 17' in the
I file's header. This option appears to be augmented each time a new
scan is started. (Thanks to S. Marrett for discovering the elusive variable.)
Without -nt option: Ifile first examines the modification time for each image and
infers from that which images form a single scan. Consecutive images that are less
than T seconds apart belong to the same scan. T is set based on the mean
time delay difference between successive images. The threshold currently
used works for the test data that we have. If it fails for your data, let us
know and supply us with the data. Once a set of images is grouped into a
scan the sequence of slice location is analysed and duplicate, missing slices,
and incomplete volumes are detected. Sets of images that do not pass these tests
Preserving Time Info: (not necessary with -nt option but does not hurt to preserve anyway)
It is important to preserve the file modification time info as you copy or untar
the data. If you neglect to do so and fail to write down where each scan ends
and/or begins, you might have a hell of a time reconstructing your data.
When copying image directories, use:
cp -rp ???/* TARGET/
and when untaring the archive on linux use:
tar --atime-preserve -xf Archive.tar
On Sun and SGI, tar -xf Archive.tar preserves the time info.
Out of justifiable laziness, and for other less convincing reasons, I have left
Ifile and @RenamePanga separate. They can be combined into one program but it's usage
would become more complicated. At any rate, the user should not notice any difference
since all they have to do is run the script GERT_reco that is created by Ifile.
Dec. 12/01 (Last modified July 24/02) SSCC/NIMH
Robert W. Cox(firstname.lastname@example.org) and Ziad S. Saad (email@example.com)
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Wed Mar 1 21:33:40 EST 2023