I’ve just recently discovered what ICC is and 3dLME, so forgive my ignorance. I am trying to compute test-retest reliability for 3 runs of resting state. The file I input is a whole brain correlation map from a seed in the left inferior frontal gyrus. I am struggling to understand the output of the command. It seems that the only output is a 3D dataset and I’m not sure how to interpret the results in the GUI. Also, is there a way to add an option to quantify values in a text file or something? Thanks so much!! Here’s my code:
I assume that you have more than two subjects as input.
It seems that the only output is a 3D dataset and I’m not sure how to interpret the results in the GUI.
There should have more than one sub-brick in the output. The one with the label ‘Subj’ is the ICC you’re looking for.
Also, is there a way to add an option to quantify values in a text file or something?
This is a whole-brain voxel-wise ICC analysis. I’m not so sure what you’re asking. If you want to the ICC for a particular list of ROIs, you can extract them from the whole brain analysis results.
I assume that you have more than two subjects as input.
Yes, I just wanted to run a dummy before inputting the larger dataset.
There should have more than one sub-brick in the output. The one with the label ‘Subj’ is the ICC you’re looking for.
So the ICC map under ‘Subj’ sub-brick can be interpreted as what? What is the typical threshold for the map?
This is a whole-brain voxel-wise ICC analysis. I’m not so sure what you’re asking. If you want to the ICC for a particular list of ROIs, you can extract them from the whole brain analysis results.
Thank you! I have a follow up question. Like I said earlier, I am trying to look at ICC across 3 runs of resting state fMRI data for 31 patients. When I run the 3dLME command, it gets killed early on. Is there a reason for this? Below the command and options I used, as well as the output:
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***** Summary information of data structure *****
31 subjects : p12 p14 p17 p22 p23 p25 p29 p3 p32 p33 p40 p43 p47 p48 p5 p64 p65 p67 p71 p73 p76 p78 p79 p80 p82 p83 p85 p86 p92 p96 p97
93 response values
3 levels for factor Cond : EC2 EC3 EO1
0 post hoc tests
Contingency tables of subject distributions among the categorical variables:
***** End of data structure information *****
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Reading input files now…
Reading input files: Done!
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
[1] “Great, test run passed at voxel (32, 57, 48)!”
[1] “Start to compute 96 slices along Z axis. You can monitor the progress”
[1] “and estimate the total run time as shown below.”
[1] “09/18/18 15:39:36.897”
Loading required package: snow
Package snow loaded successfully!
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