Hello,
I also had a question about the 3dLME output. When you specify GLTs and then generate a report, the report lists the size of the significant clusters and coordinates of the peak voxels, but is it possible to also list the t-statistics and p-values? Or is that not recommended?
Thank you, and sorry for the multiple questions!
is it possible to also list the t-statistics and p-values
In the literature people usually report t- or p-value, or both. I would report the effect estimate (beta), which shows the physical measurement, as well as the t-stat value (plus its degrees of freedom).
Thank you, I will do that. How would I generate a table with that information?
How would I generate a table with that information?
Once you set up your t-stat threshold and cluster threshold size, click “Clusterize” button on the AFNI GUI. On the popup window, change the number of “voxels” from the default of 20 to the threshold you want (e.g., from the output table of 3dClustSim). Click “Set”, and then you should be able to see those surviving clusters only. You can also click the button “Rpt” underneath “Clusterize”, and you will get a new window that tabulates the surviving clusters. You can navigate to any of those clusters by clicking buttons such as “Jump” or “Flash” on each row in the table.
On the window with the cluster table, there is a button that allows you to obtain a command with 3dclust. You can use that command on the terimal to obtain the table in text format.
Thank you. So this is the output that I get from the table. Does the “mean” represent the effect estimate (beta)? And then where can I find the t-stat and degrees of freedom?
#Cluster report for file /Applications/freesurfer/Paper1/Fixed3_ACS_PCC.nii
#[Connectivity radius = 1.01 mm Volume threshold = 162.00 ]
#[Single voxel volume = 27.0 (microliters) ]
#[Voxel datum type = float ]
#[Voxel dimensions = 3.000 mm X 3.000 mm X 3.000 mm ]
#[Coordinates Order = RAI ]
#[Fake voxel dimen = 1.000 mm X 1.000 mm X 1.000 mm ]
#Mean and SEM based on Absolute Value of 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
#------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
474 1.2 56.3 26.3 -13.5 13.5 37.5 76.5 2.5 47.5 0.0064 2.2e-04 0.0253 7.5 55.5 23.5
365 1.0 -50.8 17.5 -10.5 13.5 -64.5 -34.5 -12.5 47.5 0.0072 2.7e-04 -0.0229 -7.5 -49.5 8.5
38 0.3 24.3 32.8 -4.5 4.5 10.5 34.5 26.5 35.5 0.0049 6.0e-04 -0.0132 1.5 25.5 32.5
22 56.5 9.4 -10.4 49.5 61.5 4.5 13.5 -18.5 -6.5 0.0043 6.8e-04 -0.0108 61.5 10.5 -9.5
17 -51.5 62.7 21.2 -55.5 -46.5 58.5 67.5 14.5 29.5 0.0052 8.5e-04 0.0145 -46.5 61.5 17.5
16 49.8 58.6 22.6 46.5 52.5 55.5 61.5 11.5 29.5 0.0087 0.0016 0.0188 49.5 58.5 26.5
13 18.0 -30.8 54.1 13.5 19.5 -34.5 -28.5 47.5 59.5 0.0041 9.4e-04 0.0101 19.5 -31.5 53.5
11 -20.2 -29.3 53.7 -25.5 -13.5 -34.5 -28.5 50.5 56.5 0.0059 0.0012 0.0121 -19.5 -28.5 56.5
10 41.4 62.1 20.0 40.5 43.5 58.5 67.5 14.5 23.5 0.0027 6.9e-04 -0.006 40.5 64.5 23.5
9 -61.9 12.8 -10.1 -64.5 -61.5 10.5 16.5 -15.5 -6.5 0.0079 0.0022 0.0192 -61.5 10.5 -9.5
7 44.9 -33.7 -6.1 43.5 46.5 -37.5 -31.5 -9.5 -3.5 0.0043 9.7e-04 -0.008 43.5 -34.5 -6.5
7 0.6 -34.5 13.6 -1.5 1.5 -37.5 -31.5 8.5 14.5 0.0049 0.0016 -0.0115 1.5 -34.5 14.5
7 47.6 67.2 26.0 46.5 49.5 64.5 67.5 20.5 29.5 0.0061 0.0016 0.0122 46.5 67.5 29.5
7 16.7 -24.9 56.6 13.5 19.5 -25.5 -22.5 53.5 59.5 0.004 0.0013 -0.0106 19.5 -25.5 56.5
6 -62.0 -0.5 -19.7 -64.5 -61.5 -4.5 1.5 -21.5 -15.5 0.0069 0.0021 -0.0151 -61.5 1.5 -18.5
6 13.0 -57.8 27.8 10.5 13.5 -58.5 -55.5 23.5 32.5 0.0078 0.0022 -0.0146 13.5 -58.5 26.5
Or should I be using a different command than 3dclust? Thanks again.
Thank you. So this is the output that I get from
the table. Does the “mean” represent the effect
estimate (beta)? And then where can I find the
t-stat and degrees of freedom?#Cluster report for file
/Applications/freesurfer/Paper1/Fixed3_ACS_PCC.nii
#[Connectivity radius = 1.01 mm Volume threshold
= 162.00 ]
#[Single voxel volume = 27.0 (microliters) ]
#[Voxel datum type = float ]
#[Voxel dimensions = 3.000 mm X 3.000 mm X
3.000 mm ]
#[Coordinates Order = RAI ]
#[Fake voxel dimen = 1.000 mm X 1.000 mm X
1.000 mm ]
#Mean and SEM based on Absolute Value of 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
#------ ----- ----- ----- ----- ----- -----
474 1.2 56.3 26.3 -13.5 13.5 37.5
37.5 76.5 2.5 47.5 0.0064 2.2e-04
0.0253 7.5 55.5 23.5
365 1.0 -50.8 17.5 -10.5 13.5 -64.5
64.5 -34.5 -12.5 47.5 0.0072 2.7e-04
-0.0229 -7.5 -49.5 8.5
38 0.3 24.3 32.8 -4.5 4.5 10.5
10.5 34.5 26.5 35.5 0.0049 6.0e-04
-0.0132 1.5 25.5 32.5
22 56.5 9.4 -10.4 49.5 61.5 4.5
4.5 13.5 -18.5 -6.5 0.0043 6.8e-04
-0.0108 61.5 10.5 -9.5
17 -51.5 62.7 21.2 -55.5 -46.5 58.5
58.5 67.5 14.5 29.5 0.0052 8.5e-04
0.0145 -46.5 61.5 17.5
16 49.8 58.6 22.6 46.5 52.5 55.5
55.5 61.5 11.5 29.5 0.0087 0.0016
0.0188 49.5 58.5 26.5
13 18.0 -30.8 54.1 13.5 19.5 -34.5
-34.5 -28.5 47.5 59.5 0.0041 9.4e-04
0.0101 19.5 -31.5 53.5
11 -20.2 -29.3 53.7 -25.5 -13.5 -34.5
-34.5 -28.5 50.5 56.5 0.0059 0.0012
0.0121 -19.5 -28.5 56.5
10 41.4 62.1 20.0 40.5 43.5 58.5
58.5 67.5 14.5 23.5 0.0027 6.9e-04
-0.006 40.5 64.5 23.5
9 -61.9 12.8 -10.1 -64.5 -61.5 10.5
10.5 16.5 -15.5 -6.5 0.0079 0.0022
0.0192 -61.5 10.5 -9.5
7 44.9 -33.7 -6.1 43.5 46.5 -37.5
-37.5 -31.5 -9.5 -3.5 0.0043 9.7e-04
-0.008 43.5 -34.5 -6.5
7 0.6 -34.5 13.6 -1.5 1.5 -37.5
-37.5 -31.5 8.5 14.5 0.0049 0.0016
-0.0115 1.5 -34.5 14.5
7 47.6 67.2 26.0 46.5 49.5 64.5
64.5 67.5 20.5 29.5 0.0061 0.0016
0.0122 46.5 67.5 29.5
7 16.7 -24.9 56.6 13.5 19.5 -25.5
-25.5 -22.5 53.5 59.5 0.004 0.0013
-0.0106 19.5 -25.5 56.5
6 -62.0 -0.5 -19.7 -64.5 -61.5 -4.5
-4.5 1.5 -21.5 -15.5 0.0069 0.0021
-0.0151 -61.5 1.5 -18.5
6 13.0 -57.8 27.8 10.5 13.5 -58.5
-58.5 -55.5 23.5 32.5 0.0078 0.0022
-0.0146 13.5 -58.5 26.5
It’s hard for me to interpret the table without the command. Could you provide the 3dclust script?
Thanks, here was the command that I used (the one generated from SaveTab1)
3dclust -1Dformat -nosum -1dindex 10 -1tindex 0 -2thresh -14.82 14.82 -dxyz=1 1.01 6 /Applications/freesurfer/scripts/Worry_PCC.nii
What is the output of the following command?
3dinfo -verb /Applications/freesurfer/scripts/Worry_PCC.nii
Thanks! Here is what I get:
Last login: Wed Apr 18 14:54:25 on ttys010
[mac192047:~] ID1% 3dinfo -verb /Applications/freesurfer/scripts/Worry_PCC.nii
++ 3dinfo: AFNI version=AFNI_17.3.04 (Nov 21 2017) [64-bit]
Dataset File: /Applications/freesurfer/scripts/Worry_PCC.nii
Identifier Code: AFN_ik8qxoH6Hcmamn8XsEmGsg Creation Date: Mon Apr 16 19:51:27 2018
Template Space: TT_N27
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 8,294,400 (8.3 million [mega]) bytes
Geometry String: “MATRIX(3,0,0,-79.5,0,3,0,-79.5,0,0,3,-63.5):54,64,50”
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -79.500 [R] -to- 79.500 [L] -step- 3.000 mm [ 54 voxels]
A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -63.500 [I] -to- 83.500 [S] -step- 3.000 mm [ 50 voxels]
Number of values stored at each pixel = 12
– At sub-brick #0 ‘(Intercept) F’ datum type is float
statcode = fift; statpar = 1 20
– At sub-brick #1 ‘Session F’ datum type is float
statcode = fift; statpar = 1 16
– At sub-brick #2 ‘Worry F’ datum type is float
statcode = fift; statpar = 1 16
– At sub-brick #3 ‘Session:Worry F’ datum type is float
statcode = fift; statpar = 1 16
– At sub-brick #4 ‘T1’ datum type is float
– At sub-brick #5 ‘T1 Z’ datum type is float
statcode = fizt
– At sub-brick #6 ‘T2-T1’ datum type is float
– At sub-brick #7 ‘T2-T1 Z’ datum type is float
statcode = fizt
– At sub-brick #8 ‘T1-Worry’ datum type is float
– At sub-brick #9 ‘T1-Worry Z’ datum type is float
statcode = fizt
– At sub-brick #10 ‘Session_Worry’ datum type is float
– At sub-brick #11 ‘Session_Worry Z’ datum type is float
statcode = fizt
----- HISTORY -----
[ID1@mac192047: Mon Apr 16 19:51:27 2018] [ID1@mac192047: Mon Apr 16 18:19:21 2018] 3dLME -prefix /Applications/freesurfer/scripts/Worry_PCC.nii -jobs 1 -model ‘SessionWorry’ -resid /Applications/freesurfer/scripts/Worry_PCC_resid.nii -mask /Applications/freesurfer/scripts/template_MNI_BrainExtractionMask_2mmDil1_resampled.nii.gz -qVars Worry -qVarCetners 0 -ranEff 1+Worry -SS_type 3 -num_glt 4 -gltLabel 1 T1 -gltCode 1 Session : '1T1’ -gltLabel 2 T2-T1 -gltCode 2 Session : '-1T1’ ‘1T2’ -gltLabel 3 T1-Worry -gltCode 3 Session : '-1T1’ Worry : -gltLabel 4 Session_Worry -gltCode 4 Session : ‘-1T1’ '1T2’ Worry : -dataTable @/Applications/freesurfer/scripts/DataTables/PCCDataTable_Worry.txt
Assuming that your focus is on the effect of ‘Session_Worry’ (which is associated with sub-bricks #10 and #11), you can try something like:
3dclust -1Dformat -nosum -1dindex 10 -1tindex 11 -2thresh ? ? -dxyz=3 3.1 X
Fill the question marks with the t-stat threshold in case. The voxel size in your case is 3 x 3 x 3 mm^3. Replace “X” with the cluster size threshold.
Hi
I found this thread that answers one of my doubts and thank you very much for this. I just wanted to ask what is the number 3.1 in the command
3dclust -1Dformat -nosum -1dindex 10 -1tindex 11 -2thresh ? ? -dxyz=3 3.1 X
Also, can -1dindex & -1tindex be same (as in an F test)
Thank you so much for your help!
Sincerely
Prerona
Hi Prerona,
I just wanted to ask what is the number 3.1 in the command
3dclust -1Dformat -nosum -1dindex 10 -1tindex 11 -2thresh ? ? -dxyz=3 3.1 X
The number 3.1 is meant to provide a distance that is slightly bigger than a value per the neighborhood definition (NN1: face touching in the above example) so that 3dclust can use it as a criterion and search for surviving clusters.
Also, can -1dindex & -1tindex be same (as in an F test)
It’s reasonable in the case of F-statistic.
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