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.comwrote:

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

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

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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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_advancehttp://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

______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

--

Mr. John Griffiths, MSc

PhD Candidate

Centre for Speech, Language, and the Brain

Department of Experimental Psychology

University of Cambridge, UK

hi bruce,

sorry about the documentation snafu. i kept getting an error (having tried --help, -h, -u and all the freesurfer variants) and in the end it turned out i was operating out of a non-existent/stale directory and that's why i wasn't getting any help!

this is very much what i needed.

cheers,

satra

On Sat, Oct 6, 2012 at 4:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

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_advancehttp://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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        PhD Candidate

        Centre for Speech, Language, and the Brain

        Department of Experimental Psychology

        University of Cambridge, UK