cheers,

satra

On Sat, Oct 6, 2012 at 4:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Satra

isn't the code enough documentation enough?? You can use it in different ways. Try mris_divide_parcellation -help. You can either specify an area threshold and it will split annotations along their principle eigenaxis until they are under that (which may mean different number for different subjects), or you can give it a split file which explicitly tells it what to split (and it will do the same for each subject)

cheers
Bruce
p.s. mris_divide_parcellation -help

mris_divide_parcellation [options] subject hemi sourceannot [splitfile|areathresh] outannot

options
-help
-scale <scale> specify offset scaling for rgb values (default=20)
-l <label name> only process the label <label name> (not implemented yet)

This program divides one or more parcellations into divisions
perpendicular to the long axis of the label. The number of divisions
can be specified in one of two ways, depending upon the nature of the
fourth argument.

First, a splitfile can be specified as the fourth argument. The
splitfile is a text file with two columns. The first column is the
name of the label in the source annotation, and the second column is
the number of units that label should be divided into. The names of
the labels depends upon the source parcellation. For aparc.annot and
aparc.a2005.annot, the names can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt. For aparc.annot, the labels
are between the ranges of 1000-1034. For aparc.a2005s.annot, the
labels are between the ranges of 1100-1181. The name for the label is
the name of the segmentation without the 'ctx-lh'. Note that the name
included in the splitfile does not indicate the hemisphere. For
example, 1023 is 'ctx-lh-posteriorcingulate'. You should put
'posteriorcingulate' in the splitfile. Eg, to divide it into three
segments, the following line should appear in the splitfile:

posteriorcingulate 3

Only labels that should be split need be specified in the splitfile.

The second method is to specify an area threshold (in mm^2) as the
fourth argument, in which case each label is divided until each
subdivision is smaller than the area threshold.

The output label name will be the original name with _divN appended,
where N is the division number. N will go from 2 to the number of
divisions. The first division has the same name as the original label.

EXAMPLE:

cd $SUBJECTS_DIR/mysubj001/label

Create a split file to divide the superior frontal gyrus into 4
segements and the precentral gyrus into 3 segments:

echo superiorfrontal 4 > splittable.txt
echo precentral 3 >> splittable.txt

Run program:

mris_divide_parcellation mysubj001 rh aparc.annot splittable.txt rh.aparc.split-sfg+pc

This reads in rh.aparc.annot, splits the SFG and PC, and and saves the
result to rh.aparc.split-sfg+pc

View

tksurfer mysubj001 rh inflated -annot aparc.split-sfg+pc

The SFG divisions will have the following names: superiorfrontal,
superiorfrontal_div2, superiorfrontal_div3, superiorfrontal_div4. The
PC divisions will be precentral, precentral_div2, precentral_div3.

On Sat, 6 Oct 2012, Satrajit Ghosh wrote:

hi bruce,
I'm not positive I understand what you want. Have you tried
mris_divide_parcellation?

how do i use mris_divide_parcellation? any documentation somewhere?

the basic idea is to create some form of voronoi tesselation of a region
constrained by a parameter n_sub_regions.

subj1: aparc.annot -> e.g i want to break up stg into 6 regions
subj2: break up stg also into 6 regions such that there is a one to one
correspondence between the subj2 regions and subj1 regions.

cheers,

satra

Bruce
On Wed, 3 Oct 2012, Satrajit Ghosh wrote:

hi john,
thanks. that's the idea, but what i want is that
sub-division is done within
regions that are either determined automatically
through the freesurfer
classifier or through manual parcellations. not a
fixed template of parcels
that's transferred via the spherical registration.

cheers,

satra

On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths
<j.davidgriffiths@gmail.com>
wrote:

Would the Lausanne2008 template from the connectome
mapping toolkit
not do the trick?

http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advance

d.html

On 3 October 2012 23:18, Satrajit Ghosh
<satra@mit.edu> wrote:
hi bruce,
is there a way to divide consistently (same number
of regions
and one to one correspondence - obviously not the
exact same
areas) across subjects within aparc regions?

cheers,

satra

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