#------------------------------------------------------------------------
Simple script to test what 'flip', if any, should likely be
performed for a data set when using 1dDW_Grad_o_Mat++.
**Majorly updated in Jan, 2017-- otherwise you wouldn't even be
reading this help file description!**
When using this function and looking at the number of tracts per
flip, there should be a *very* clear winner. If there isn't, then
probably something is not correct in the data (something
inconsistent in bvals or bvecs, large noise, etc.). Please make
sure to look at the results in SUMA when prompted at the end, to
make sure that everything makes sense!
ver 3.1; revision date Feb 12, 2019.
Written by PA Taylor (NIH).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
OUTPUT
On a good day, this function will:
+ Recommend using either '-no_flip', or one
of the {-flip_x|-flip_y|-flip_z} options for 1dDW_Grad_o_Mat++.
+ It will store this snippet of code in a file called
(default name), which the User could be used in scripting later.
+ It will produce a temporary working directory called
'_tmp_TESTFLIP/' to store intermediate files, of which there are
many (could be wiped away with '-do_clean').
+ It will also prompt you, O User, to visually check the
tract results with some simple example scripts (some day it might
automatically make snapshots!).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
COMMAND
@GradFlipTest \
-in_dwi DWI \
{ -in_row_vec | -in_col_vec | -in_col_matA | -in_col_matT } FF \
{ -mask MASK } \
{ -in_bvals BB } \
{ -alg_Thresh_FA X } \
{ -alg_Thresh_Len L } \
{ -prefix PPP } \
{ -scale_out_1000 } \
{ -wdir WWW } \
{ -do_clean }
USAGE
(*must* input 1 set of DWIs *and* 1 set of grads-- choice of format):
-in_dwi DWI :set of DWIs (N total volumes)
-in_row_vec FF :set of row-wise gradient vectors
-in_col_vec FF :set of column-wise gradient vectors
-in_col_matA FF :set of column-wise g- or b-matrix elements
("AFNI"-style format, "diagonal-first")
-in_col_matT FF :set of column-wise g- or b-matrix elements
("TORTOISE"-style format, "row-first")
-mask MASK :option mask (probably whole brain); otherwise,
automasking is performed
-in_bvals BB :can input bvals, as in 1dDW_Grad_o_Mat++, if
necessary (but shouldn't be necessary?)
-alg_Thresh_FA X :set minimum FA value for tracking (default X=0.2
as for adult, healthy WM parenchyma)
-alg_Thresh_Len L :set minimum tract length to require to keep a tract
when propagating (default L=30mm ; probably want it
to be a bit on the longside for clear counting and
comparison)
-prefix PPP :output name of text file that stores recommended
flip opt (default is ). This option is now
also used to determine the directory for all outputs
of this program, via the path of PPP.
NB: The previous, separate option for specifying output directory
was '-outdir OUT', but this no longer is used; the path of an
output directory is specified by taking the path-part of the
'-prefix PPP' input.
-check_abs_min VVV :briefly, this can help the program push through
finding tiny negative values (that miiiight be
due to rounding errors or small numerical
things) in columns that should only contain
numbers >=0. 'VVV' is basically a tolerance for
the magnitude of negative values you are willing
to allow: anything between [-VVV, 0) gets zeroed
for further calcs. See 1dDW_Grad_o_Mat++'s help
for more information on this option (of the same
name).
-scale_out_1000 :as in 3dDWItoDT. Probably not necessary, since we
are just checking out trackability
-wdir WWW :rename working directory output; useful if running
multiple iterations. Default: _tmp_TESTFLIP.
NB: WWW should *only* be the name of the directory,
not contain path info-- the location of WWW is just
determined by the path for output, which comes from
the path part of PPP/
-do_clean :remove temporary directory
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
EXAMPLES
@GradFlipTest \
-in_dwi DWI.nii.gz \
-in_col_matA BMTXT_AFNI.txt
or (perhaps if scanning infants, who have less developed myelin)
@GradFlipTest \
-in_dwi DWI.nii.gz \
-in_col_vec GRADS.txt \
-mask mask_DWI.nii.gz \
-alg_Thresh_FA 0.1
