Dear Rick,
I put the name very strangely.
The Run_all_mean+orig was the mean of three mask (because there are three runs) using:
3dMean -datum short -prefix Run_all_mean Run1_mask+orig.HEAD Run2_mask+orig.HEAD Run3_mask+orig.HEAD
I am sorry to make you confusing again.
But, I think I did as you mentioned.
I used the 3dDeconvolve:
3dDeconvolve -xout -input Run_all_3dtcat+orig.HEAD -polort 2 -mask Run_all_3dcalc+orig -num_stimts 3 -stim_file 1 aut_HRF.1D -stim_label 1 aut -stim_file 2 con_HRF.1D -stim_label 2 con -stim_file 3 ext_HRF.1D -stim_label 3 ext -concat runs.1D -full_first -fout -tout -bucket motivation -glt 1 glt.mat -glt_label 1 "aut_con" -glt 1 glt2.mat -glt_label 2 "con_aut" -glt 1 glt3.mat -glt_label 3 "ext_con" -glt 1 glt4.mat -glt_label 4 "con_ext" -glt 1 glt5.mat -glt_label 5 "aut_ext" -glt 1 glt6.mat -glt_label 6 "ext_aut"
At the time, I used –polort 2 and –concat runs.1D.
The runs.1D was 0 300 600 because each run had 300 scans.
The results of the 3dinfo of Run1_3dcalc+orig were;
Dataset File: Run1_3dcalc+orig
Identifier Code: XYZ_lqBl52_ijthArOZt_KaG-g Creation Date: Thu Sep 25 15:06:18 2008
Dataset Type: Fast Spin Echo (-fse)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 688128000 (688 million) bytes
Geometry String: "MATRIX(2,0,0,-121.3983,0,2,0,-141.0593,0,0,-2,91.17918):128,128,70"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Superior-to-Inferior [-orient RAS]
R-to-L extent: -121.398 [R] -to- 132.602 [L] -step- 2.000 mm [128 voxels]
A-to-P extent: -141.059 [A] -to- 112.941 [P] -step- 2.000 mm [128 voxels]
I-to-S extent: -46.821
-to- 91.179 [S] -step- 2.000 mm [ 70 voxels]
Number of time steps = 300 Time step = 2.000s Origin = 0.000s
-- At sub-brick #0 '#0' datum type is short: 0 to 32767 [internal]
[* 0.00451115] 0 to 147.817 [scaled]
-- At sub-brick #1 '#1' datum type is short: 0 to 32767 [internal]
[* 0.00440748] 0 to 144.42 [scaled]
-- At sub-brick #2 '#2' datum type is short: 0 to 32767 [internal]
[* 0.00423611] 0 to 138.805 [scaled]
** For info on all 300 sub-bricks, use '3dinfo -verb' **
----- HISTORY -----
[woogul@woogul: Thu Sep 25 15:06:18 2008] ===================================
[woogul@woogul: Thu Sep 25 15:06:18 2008] === History of inputs to 3dcalc ===
[woogul@woogul: Thu Sep 25 15:06:18 2008] === Input a:
[woogul@woogul: Thu Sep 25 15:06:18 2008] [woogul@woogul: Thu Sep 25 13:44:09 2008] to3d -fim -prefix Run1 -orient RAS -view orig -time:zt 16 300 2000ms seq+z MR_0004_0001.dcm MR_0004_0002.dcm MR_0004_0003.dcm ... MR_0004_0299.dcm MR_0004_0300.dcm
[woogul@woogul: Thu Sep 25 13:50:11 2008] 3dTshift -verbose -tzero 0 -quintic -prefix Run1_3dtshift Run1+orig
[woogul@woogul: Thu Sep 25 13:51:22 2008] 3dAllineate -master anat_skullstrip+orig -mast_dxyz 2.0 -1Dmatrix_apply as_to_v2.aff12.1D -input Run1_3dtshift+orig -final quintic -prefix Run1_3dvolreg
[woogul@woogul: Thu Sep 25 14:11:25 2008] 3dmerge -doall -prefix Run1_smooth -1blur_fwhm 8 Run1_3dvolreg+orig
[woogul@woogul: Thu Sep 25 15:06:18 2008] === Input b:
[woogul@woogul: Thu Sep 25 15:06:18 2008] [woogul@woogul: Thu Sep 25 13:44:09 2008] to3d -fim -prefix Run1 -orient RAS -view orig -time:zt 16 300 2000ms seq+z MR_0004_0001.dcm MR_0004_0002.dcm MR_0004_0003.dcm ... MR_0004_0299.dcm MR_0004_0300.dcm
[woogul@woogul: Thu Sep 25 13:50:11 2008] 3dTshift -verbose -tzero 0 -quintic -prefix Run1_3dtshift Run1+orig
[woogul@woogul: Thu Sep 25 13:51:22 2008] 3dAllineate -master anat_skullstrip+orig -mast_dxyz 2.0 -1Dmatrix_apply as_to_v2.aff12.1D -input Run1_3dtshift+orig -final quintic -prefix Run1_3dvolreg
[woogul@woogul: Thu Sep 25 14:11:25 2008] 3dmerge -doall -prefix Run1_smooth -1blur_fwhm 8 Run1_3dvolreg+orig
[woogul@woogul: Thu Sep 25 15:00:23 2008] 3dTstat -prefix Run1_mean Run1_smooth+orig
[woogul@woogul: Thu Sep 25 15:06:18 2008] === Input c:
[woogul@woogul: Thu Sep 25 15:06:18 2008] [woogul@woogul: Thu Sep 25 13:44:09 2008] to3d -fim -prefix Run1 -orient RAS -view orig -time:zt 16 300 2000ms seq+z MR_0004_0001.dcm MR_0004_0002.dcm MR_0004_0003.dcm ... MR_0004_0299.dcm MR_0004_0300.dcm
[woogul@woogul: Thu Sep 25 13:50:11 2008] 3dTshift -verbose -tzero 0 -quintic -prefix Run1_3dtshift Run1+orig
[woogul@woogul: Thu Sep 25 13:51:22 2008] 3dAllineate -master anat_skullstrip+orig -mast_dxyz 2.0 -1Dmatrix_apply as_to_v2.aff12.1D -input Run1_3dtshift+orig -final quintic -prefix Run1_3dvolreg
[woogul@woogul: Thu Sep 25 14:11:25 2008] 3dmerge -doall -prefix Run1_smooth -1blur_fwhm 8 Run1_3dvolreg+orig
[woogul@woogul: Thu Sep 25 14:50:52 2008] 3dAutomask -dilate 1 -prefix Run1_mask Run1_smooth+orig
[woogul@woogul: Thu Sep 25 14:57:14 2008] 3dMean -datum short -prefix Run_all_mean Run1_mask+orig.HEAD Run2_mask+orig.HEAD Run3_mask+orig.HEAD
[woogul@woogul: Thu Sep 25 15:06:18 2008] ===================================
[woogul@woogul: Thu Sep 25 15:06:18 2008] 3dcalc -a Run1_smooth+orig -b Run1_mean+orig -c Run_all_mean+orig -expr 'c * min(200, a/b*100)' -prefix Run1_3dcalc
In fact, the reason why I wanted to do the functional ROI was that I wanted to compare activations of all conditions.
For example, there is an “a” activation in “A” condition – “C” condition but no “a” activation in “B” –“C”.
In this situation, I wanted to know the magnitude of the signal of “a” in “B” condition even though there is no activation in order to compare “a” activities among “A”, “B”, and “C” conditions.
I don’t have to focus on the ROIs with activated regions.
If there is an easier way to reach the goal that I mentioned above, I can use it.
Then, for my goal, is the ROIs with atlas the better way?
Thanks.
Woogul Lee
