Hi Daniel,
Thanks for your help. When I use the prefix option in the 3dclust command, the overlay is perfect - it has the activation cluster I am looking for. But again, this doesn't seem to match up with the output of the 3dclust command.
My activation, using the whereami command, says it is approximately 48 -59, -14 LPI T&T coordinates.
I have posted a copy of the output from 3dclust. Also, I have attached the 3dinfo results of decon_1_results+orig below. I'm still concerned about this possibly being a problem with the overall coordinate system - when I try to 'jump' to a coordinate, it sends me to the wrong place. I noticed that in the 3dinfo it says the block_1_results+orig dataset is in RAI coordinates. Possibly this is the problem?
Thanks,
Victor
#Cluster report for file decon_1_results+orig
#[Connectivity radius = 5.00 mm Volume threshold = 537.11 ]
#[Single voxel volume = 48.8 (microliters) ]
#[Voxel datum type = short ]
#[Voxel dimensions = 3.125 mm X 3.125 mm X 5.000 mm ]
#[Coordinates Order = LPI ]
#Mean and SEM based on Absolute Value of voxel intensities:
#
#Volume CM LR CM PA CM IS minLR maxLR minPA maxPA minIS maxIS Mean SEM Max Int MI LR MI PA MI IS
#------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
*+ WARNING: changed output dataset name from 'bloc_clust' to 'bloc_clust_AA2'
++ Wrote dataset ./bloc_clust_AA2+orig.BRIK
2295 21.4 -60.9 32.3 2.7 40.2 -69.9 -44.9 21.1 36.1 0.0818 0.0037 0.1559 12.1 -66.8 36.1
2246 43.9 -18.1 27.8 34.0 55.9 -32.4 -10.6 16.1 46.1 0.0798 0.0028 0.1241 52.7 -13.7 21.1
1172 18.3 -42.5 63.2 5.9 30.9 -48.1 -35.6 56.1 66.1 0.0692 0.0033 0.1135 24.6 -38.7 66.1
977 34.5 -42.8 19.5 24.6 43.4 -48.1 -38.7 16.1 31.1 0.068 0.0027 0.1004 34.0 -41.8 16.1
830 32.1 12.8 57.4 21.5 37.1 11.3 17.6 51.1 66.1 0.0653 0.0024 0.0893 24.6 11.3 56.1
781 36.9 -36.9 6.6 24.6 46.5 -41.8 -32.4 1.1 11.1 0.0623 0.0022 0.0799 43.4 -35.6 6.1
781 -48.0 33.6 30.0 -50.4 -44.1 26.9 36.3 21.1 36.1 0.0719 0.0045 0.1152 -47.3 33.2 26.1
732 25.5 -53.2 3.7 15.2 34.0 -60.6 -48.1 1.1 11.1 0.0629 0.0021 0.0802 24.6 -57.4 1.1
586 45.5 36.0 22.0 40.2 49.6 30.1 42.6 16.1 26.1 0.0624 0.0019 0.0744 49.6 30.1 26.1
586 -55.9 -16.3 20.3 -62.9 -47.3 -19.9 -13.7 16.1 26.1 0.0618 0.002 0.0777 -59.8 -16.8 21.1
#------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
# 10986 21.9 -27.6 30.7 0.0721 0.0012
3dinfo output:
Dataset File: decon_1_results+orig
Identifier Code: XYZ_DHkR5pufD966siFzM2beGw Creation Date: Thu Aug 9 15:50:33 2007
Dataset Type: Func-Bucket (-fbuc)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -93.375 [R] -to- 103.500 [L] -step- 3.125 mm [ 64 voxels]
A-to-P extent: -108.188 [A] -to- 88.687 [P] -step- 3.125 mm [ 64 voxels]
I-to-S extent: -48.882
-to- 86.118 [S] -step- 5.000 mm [ 28 voxels]
Number of values stored at each pixel = 10
-- At sub-brick #0 'Full_R^2' datum type is short: 0 to 32767 [internal]
[* 4.75723e-06] 0 to 0.15588 [scaled]
statcode = fibt; statpar = 0.5 91
-- At sub-brick #1 'Full_Fstat' datum type is short: 0 to 32767 [internal]
[* 0.0010257] 0 to 33.6092 [scaled]
statcode = fift; statpar = 1 182
-- At sub-brick #2 'face#0_Coef' datum type is short: -14749 to 32767 [internal]
[* 3.08065e-07] -0.00454365 to 0.0100944 [scaled]
-- At sub-brick #3 'face#0_Tstat' datum type is short: -30713 to 32767 [internal]
[* 0.000176926] -5.43394 to 5.79735 [scaled]
statcode = fitt; statpar = 182
-- At sub-brick #4 'face_R^2' datum type is short: 0 to 32767 [internal]
[* 4.75723e-06] 0 to 0.15588 [scaled]
statcode = fibt; statpar = 0.5 91
-- At sub-brick #5 'face_Fstat' datum type is short: 0 to 32767 [internal]
[* 0.0010257] 0 to 33.6092 [scaled]
statcode = fift; statpar = 1 182
-- At sub-brick #6 'facevsarrow_GLT#0_Coef' datum type is short: -14749 to 32767 [internal]
[* 3.08065e-07] -0.00454365 to 0.0100944 [scaled]
-- At sub-brick #7 'facevsarrow_GLT#0_Tstat' datum type is short: -30713 to 32767 [internal]
[* 0.000176926] -5.43394 to 5.79735 [scaled]
statcode = fitt; statpar = 182
-- At sub-brick #8 'facevsarrow_GLT_R^2' datum type is short: 0 to 32767 [internal]
[* 4.75723e-06] 0 to 0.15588 [scaled]
statcode = fibt; statpar = 0.5 91
-- At sub-brick #9 'facevsarrow_GLT_Fstat' datum type is short: 0 to 32767 [internal]
[* 0.0010257] 0 to 33.6092 [scaled]
statcode = fift; statpar = 1 182
----- HISTORY -----
[vol@floater2: Wed Aug 8 15:14:58 2007] ===================================
[vol@floater2: Wed Aug 8 15:14:58 2007] === History of inputs to 3dcalc ===
[vol@floater2: Wed Aug 8 15:14:58 2007] === Input a:
[vol@floater2: Wed Aug 8 15:14:58 2007] [vol@floater2: Thu Aug 2 13:32:41 2007] to3d -epan -prefix run1 -time:zt 28 195 2000 alt+z -xFOV 94.93743000R-105.06257000L -yFOV 109.75011000A-90.24989000P -zFOV 51.38220000I-88.61780000S OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571083349760758 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571283091860872 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571483224360986 ... OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.200707301503371944582760 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.
35120.3.2007073015033899013482874
[vol@floater2: Thu Aug 2 13:32:45 2007] [siemenstoafni rotation (12.89356457R 1.02320735A 0)]
[vol@floater2: Wed Aug 8 13:37:04 2007] 3D Registration {Datasets: Input=CON852Jul30_2007/afdir/run1+orig.HEAD; Output=Rrun1} {Parameters: Base Brick=50; Resampling=Fourier} {Basis: Dataset=CON852Jul30_2007/afdir/run1+orig.HEAD} {Outputs: dfile=Rrun1; 1Dfile=Rrun1; Graph=No}
[vol@floater2: Wed Aug 8 14:23:53 2007] 3dmerge -1blur_fwhm 4 -doall -prefix Brun1 Rrun1+orig
[vol@floater2: Wed Aug 8 15:14:58 2007] === Input b:
[vol@floater2: Wed Aug 8 15:14:58 2007] [vol@floater2: Thu Aug 2 13:32:41 2007] to3d -epan -prefix run1 -time:zt 28 195 2000 alt+z -xFOV 94.93743000R-105.06257000L -yFOV 109.75011000A-90.24989000P -zFOV 51.38220000I-88.61780000S OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571083349760758 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571283091860872 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073014571483224360986 ... OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.200707301503371944582760 OB-AX_ep2d_bold_run1/MR.1.3.12.2.1107.5.2.32.35120.3.2007073015033899013482874
[vol@floater2: Thu Aug 2 13:32:45 2007] [siemenstoafni rotation (12.89356457R 1.02320735A 0)]
[vol@floater2: Wed Aug 8 13:37:04 2007] 3D Registration {Datasets: Input=CON852Jul30_2007/afdir/run1+orig.HEAD; Output=Rrun1} {Parameters: Base Brick=50; Resampling=Fourier} {Basis: Dataset=CON852Jul30_2007/afdir/run1+orig.HEAD} {Outputs: dfile=Rrun1; 1Dfile=Rrun1; Graph=No}
[vol@floater2: Wed Aug 8 14:23:53 2007] 3dmerge -1blur_fwhm 4 -doall -prefix Brun1 Rrun1+orig
[vol@floater2: Wed Aug 8 14:37:26 2007] 3dTstat -prefix mean_run1 'Brun1+orig[5..$]'
[vol@floater2: Wed Aug 8 15:14:58 2007] ===================================
[vol@floater2: Wed Aug 8 15:14:58 2007] 3dcalc -a Brun1+orig -b mean_run1+orig -expr '(a/b*100)*step(b-301)' -prefix scaled_run1
[vol@floater2: Thu Aug 9 15:50:33 2007] 3dDeconvolve -input scaled_run1+orig -mask mask_run1+orig -censor censor.1D -polort 1 -num_stimts 1 -stim_file 1 hrfC1_idealfile.1D -stim_label 1 face -stim_minlag 1 0 -stim_maxlag 1 0 -num_glt 1 -glt 1 c1vbase.glt -glt_label 1 facevsarrow -iresp 1 irf_facevsarrow.irf -fitts full_model.fit -errts residual_error.fit -fout -tout -rout -bucket block_decon_results
[vol@floater2: Thu Aug 9 15:50:33 2007] Output prefix: decon_1_results
