I would probably use --ocn with mri_volcluster to create a single volume
in which each voxel value is the cluster number it belongs to. Then
split them out like:
mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh
doug
Gregory Dierksen wrote:
Hi,
I'm trying to use the mri_volcluster command to make label files from
a single volume of binary voxel clusters. Once I have split the
volume into individual label files I want to convter the label files
back into individual cluster volumes (I am trying to use mri_label2vol
to do this). The commands I've been using are:
mri_volcluster --in microbleeds-reslice.mgz --allowdiag --thmin .5
--labelbase ../scripts/clusters/testing/cluster
mri_label2vol --label ../scripts/clusters/testing/cluster-0001.label
--temp orig-flip-reslice.mgz --o cluster-0001.mgz
(NOTE: the -reslice is because these volumes have been resliced from
0.4492, 0.4492, 6.0000 sized voxels to conform to 1 mm^3 sized voxels;
the dimensions of the image were altered as well, from 384 x 512 x 23
voxels to 173 x 230 x 138 voxels)
When I view cluster-0001.mgz with tkmedit the result is a 3D
checkerboard like pattern with no two voxels having common edges
(despite the original cluster in microbleeds-reslice.mgz being a solid
cluster of 90 mm^3). What I wanted to see was that each cluster could
be reconstructed in a single volume (i.e. cluster-0001.mgz,
cluster-0002.mgz, etc with each volume containing only one cluster).
Also, when I use mri_cor2label and then mri_label2vol to switch
between label files and volumes files, the clusters (despite not being
split up like I want) are solid and do not display this checkerboard
effect...leading me to think that its an issue with mri_volcluster.
Any help you can offer would be great. Thanks.
Greg
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
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