7.1.34. 3dAFNItoNIFTIΒΆ

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++ 3dAFNItoNIFTI: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] Usage: 3dAFNItoNIFTI [options] dataset Reads an AFNI dataset, writes it out as a NIfTI-1.1 file.

NOTES: * The nifti_tool program can be used to manipulate

the contents of a NIfTI-1.1 file.
  • The input dataset can actually be in any input format

    that AFNI can read directly (e.g., MINC-1).

  • There is no 3dNIFTItoAFNI program, since AFNI programs

    can directly read .nii files. If you wish to make such a conversion anyway, one way to do so is like so:

3dcalc -a ppp.nii -prefix ppp -expr ‘a’
OPTIONS:
-prefix ppp = Write the NIfTI-1.1 file as ‘ppp.nii’.
Default: the dataset’s prefix is used.
  • You can use ‘ppp.hdr’ to output a 2-file NIfTI-1.1 file pair ‘ppp.hdr’ & ‘ppp.img’.
  • If you want a compressed file, try using a prefix like ‘ppp.nii.gz’.
  • Setting the Unix environment variable AFNI_AUTOGZIP to YES will result in all output .nii files being gzip-ed.
-verb = Be verbose = print progress messages.
Repeating this increases the verbosity (maximum setting is 3 ‘-verb’ options).
-float = Force the output dataset to be 32-bit
floats. This option should be used when the input AFNI dataset has different float scale factors for different sub-bricks, an option that NIfTI-1.1 does not support.

The following options affect the contents of the AFNI extension field that is written by default into the NIfTI-1.1 header:

-pure = Do NOT write an AFNI extension field into
the output file. Only use this option if needed. You can also use the ‘nifti_tool’ program to strip extensions from a file.
-denote = When writing the AFNI extension field, remove
text notes that might contain subject identifying information.
-oldid = Give the new dataset the input dataset’s
AFNI ID code.
-newid = Give the new dataset a new AFNI ID code, to
distinguish it from the input dataset.

**** N.B.: -newid is now the default action.

++ Compile date = Dec 16 2015

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