Hi all,

I've drawn anatomical masks in voxbo, converted them to nifti and then to Analyze format. When I overlay the masks on my functional in Analyze format in fslview everything looks fine. However if I convert my functionals and masks to afni, the masks are on the correct hemisphere but are in the wrong location and smaller than they should be. I think the scaling is wrong. 3dinfo for my functional gives me

++ 3dinfo: AFNI version=AFNI_2009_12_31_1431 (Feb 19 2010) [32-bit]

Dataset File: 01Visac_all+orig
Identifier Code: XYZ_5IN0zYaaEMz1rj9JdLq1qA Creation Date: Mon Sep 28 11:43:36 2009
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 612368384 (612 million) bytes
Geometry String: "MATRIX(3,0,0,-94.5,0,-3,0,94.5,0,0,3,-46.5):64,64,32"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -94.500 [R] -to- 94.500 [L] -step- 3.000 mm [ 64 voxels]
A-to-P extent: -94.500 [A] -to- 94.500 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -46.500 -to- 46.500 [S] -step- 3.000 mm [ 32 voxels]
Number of time steps = 1168 Time step = 1.75000s Origin = 0.00000s Number time-offset slices = 32 Thickness
-- At sub-brick #0 'sbrt01Visac_[0]' datum type is float: 0 to 26089.1
keywords = sbrt01Visac_Run1+orig[0]
-- At sub-brick #1 'sbrt01Visac_[1]' datum type is float: 0 to 25624.8
keywords = sbrt01Visac_Run1+orig[1]
-- At sub-brick #2 'sbrt01Visac_[2]' datum type is float: 0 to 25530.1
keywords = sbrt01Visac_Run1+orig[2]
** For info on all 1168 sub-bricks, use '3dinfo -verb' **
----- HISTORY -----
[julia@viper4th.psych.nyu.edu: Mon Sep 28 11:43:36 2009] 3dTcat -prefix 01Visac_all+orig sbrt01Visac_Run1+orig.B

3dinfo for my masks gives me:

++ 3dinfo: AFNI version=AFNI_2009_12_31_1431 (Feb 19 2010) [32-bit]

Dataset File: l_FEF_anat_mask+orig
Identifier Code: XYZ_fkjOsEXaWeTrplECk0sdsQ Creation Date: Thu Feb 25 20:11:06 2010
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 262144 (262 thousand) bytes
Geometry String: "MATRIX(1,0,0,-31.5,0,-1,0,31.5,0,0,1,-15.5):64,64,32"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -31.500 [R] -to- 31.500 [L] -step- 1.000 mm [ 64 voxels]
A-to-P extent: -31.500 [A] -to- 31.500 [P] -step- 1.000 mm [ 64 voxels]
I-to-S extent: -15.500 -to- 15.500 [S] -step- 1.000 mm [ 32 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 1

----- HISTORY -----
[kli-lab@Herkules: Thu Feb 25 20:11:06 2010] to3d -epan -prefix l_FEF_anat_mask -view orig -orient R

So the dimensions extents mismatch. Can you help?

Thanks,

Julia