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 <fis...@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.davidgriffi...@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<http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advance> >> >> d.html >> >> >> >> On 3 October 2012 23:18, Satrajit Ghosh >> <sa...@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/** >> freesurfer <https://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/**complianceline<http://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 >> >> >> >> >> >> >>
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