Dear Bruce, Many thanks for quick reply. Actually, I meant doing the same thing as you explained with mris_make_face_parcellation command .
with mris_divide_parcellation, I have done what you told me but the problem is that it only divide the labels perpendicular to the axis of the label which does not look nice. I prefer to use mris_make_face_parcellation and do for a certain label like superior temporal. Is that possible?
Thanks, Fahimeh ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, October 06, 2016 4:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_divide_parcellation
Hi Fahimeh
you can also give mris_divide_parcellation a "splitfile" :
rst, 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.
cheers Bruce On Thu, 6 Oct 2016, Mamashli, Fahimeh wrote:
Hi, Thanks for your help. I tried and it worked. However, the problem is that this is doing for all brain and it is very hard to find out which label belongs to which parcellation in the brain. For example, I am interested only to superior temporal area of the brain and I don't need rest of the brain. How can I figure out which of these labels belong to superior temporal? is there any way to do this for a certain parcellation like lh.aparc.annot ?
Thank you, Fahimeh
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2016 6:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_divide_parcellation
how would you like them divided? You can also use mris_make_face_parcellation to make units of approximately equal area (either in the individual or in the group) On Fri, 16 Sep 2016, Mamashli, Fahimeh wrote:
Dear Freesurfer group, I am going to divide a brain parcellation into divisions using mris_divide_parcellation. As far as I know from the help comment, this function "divides one or more parcellations into divisions perpendicular to the long axis of the label". Is there any other program that does not make the divisions perpendicular to the long axis?
Thank you, Fahimeh
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