desphinxify

Overview

This is a simple program that *might* be useful for desphinxifying
datasets. That is, when datasets are acquired in "sphinx" position,
this will try to reorient them to match with axial/coronal/sagittal
definitions standard to human neuroimaging. This may be useful
particularly when processing nonhuman datasets

Importantly, this program really only reliable **if** the user knows
the correct final dataset orientation, to verify. We can recommend a
useful intermediate orientation to reorient the data correctly, but
the user is in charge of being user.

ver  = 0.0
auth = PA Taylor (SSCC, NIMH, NIH)

Options

-input II         :(req) input dset name

-prefix PP        :(req) output dset name (can include path)

-orient_mid OM    :(req) intermediate orientation value, which determines
                   how the input dataset is effectively rotated (from
                   RAI orientation) in order to desphinxify it.
                   **NB:** a commonly used value here is: RIP.
                   However, users must verify this, particularly to get
                   left and right correct (other mistakes in orientation
                   tend to be more visually apparent). That is why there is
                   no default value: please check this with a pilot dataset
                   for your study.

-workdir WD      : working directory name (just name, no path;
                   will be subdirectory of the output location)

-overwrite       : when writing output, overwrite any preexisting
                   dataset (def: do not overwrite)

-no_clean        : when done, do not remove temporary working
                   directory (def: do remove woroking directory

-echo            : run very verbosely (with 'set echo' on)

-ver             : display program version

-help            : show help

-hview           : show help in text editor

Examples

1) Basic usage:

     desphinxify                                \
        -orient_mid  RIP                        \
        -input       sub-001_T1w.nii.gz         \
        -prefix      sub-001_T1w_DSPH.nii.gz

   ... and verify/validate results, for a given collection protocol.