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 RPI \
-input sub-001_T1w.nii.gz \
-prefix sub-001_T1w_DSPH.nii.gz
