Hi,
I am interested in using 3dclust to provide a fast and objective measure of the anatomical spread or extent of activated voxels in a certain region of cortex (to p <.001 uncorrected, which implies a z-t threshold of about 3.9)
We collect 24 2.0 gapless slices in the axial plane, resulting in a native EPIRT voxel size of 3.75 X 3.75 X 2.0
I wrote the following script:
*****
#! /bin/csh
# warp each subject's activation map into talairach space
foreach subject ( ao )
cd ../${subject}*
if ( -e zantfbkregdsbpf+tlrc.BRIK ) then
rm -rf zantfbkregdsbpf+tlrc.*
endif
adwarp -apar mergestruct+tlrc -dpar zantvsfbkregdsbpf+orig -prefix zantvsfbkregdsbpf
# create artificial isotropic 2mm voxels by reducing the in-plane voxel dimension to equal the 2.0 mm through-plane (slice thickness)
3drefit -xdel 2.0 -ydel 2.0 -zdel 2.0 zantvsfbkregdsbpf+tlrc
# acquire output of details of clusters of activity with connectivity distance 2.9 to get in-plane diagonal neighbors and rect neighbors
if ( -e voxelcount ) then
rm -rf voxelcount
3dclust -noabs -1thresh 3.8 2.9 500 zantvsfbkregdsbpf+tlrc > voxelcount
# restore original epirt voxel dimensions (if keeping the +tlrc file is desired)
# 3drefit -xdel 3.75 -ydel 3.75 -zdel 2.0 zantvsfbkregdsbpf+tlrc
# erase memory-hungry t-warped files
rm -rf zantvsfbkregdsbpf+tlrc.*
cd ../scripts
end
******
in order to dump out the data to file without haveing the +tlrc functional datasets lingering around using up large amounts of HD space.
Problem is, the result yields coordinates of "activated clusters" that could not be true. e.g.
Cluster report for file zantvsfbkregdsbpf+tlrc
[Connectivity radius = 2.90 mm Volume threshold = 504.00 ]
[Single voxel volume = 8.0 (microliters) ]
[Voxel datum type = short ]
[Voxel dimensions = 2.000 mm X 2.000 mm X 2.000 mm ]
Mean and SEM based on Signed voxel intensities:
Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS
------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
1248392 86.5 52.4 37.0 -58.0 240.0 -80.0 276.0 -25.0 117.0 -0.4006 0.0248 64.729 30.0 -20.0 -11.0
199616 57.4 187.7 136.3 -68.0 192.0 34.0 274.0 79.0 169.0 -1.6615 0.0358 -13.678 52.0 240.0 155.0
16432 182.4 221.4 126.4 170.0 200.0 184.0 238.0 107.0 155.0 -6.4797 0.0563 -16.324 182.0 222.0 121.0
12240 52.3 181.0 89.5 34.0 76.0 154.0 204.0 69.0 109.0 -5.0226 0.0235 -9.1499 54.0 182.0 97.0
11856 -49.4 110.8 101.7 -74.0 -30.0 84.0 136.0 83.0 115.0 5.1534 0.0272 9.1664 -46.0 124.0 111.0
10376 194.1 73.6 97.8 178.0 222.0 46.0 100.0 63.0 113.0 4.0676 0.0614 6.8243 208.0 72.0 97.0
10304 78.2 126.1 97.3 58.0 94.0 98.0 152.0 85.0 109.0 5.361 0.0336 9.5372 74.0 136.0 91.0
10056 -1.0 199.9 109.4 -18.0 20.0 166.0 224.0 85.0 125.0 5.545 0.044 13.16 -8.0 198.0 113.0
9464 140.2 131.8 54.9 126.0 154.0 114.0 150.0 33.0 83.0 -4.9266 0.0296 -9.4589 144.0 124.0 39.0
8776 186.3 128.8 124.6 160.0 218.0 106.0 150.0 113.0 133.0 5.4116 0.0394 9.498 190.0 134.0 129.0
*****
(refer to the last three columns of each line- "MI" = mm?)
What might be going on here?
