Back to PLS HelpPreprocessing and TR er-fMRI questions
Posted on 04/22/09 12:31:56
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Hi!
I am hoping to put a event-related fMRI dataset into PLS. I have two questions:
1. In pre-processing the data I performed motion correction and signal normalization in AFNI. I have this either for each of 3 runs, or concatenated into 1 run. When changing these into .nii files for PLS, is it best to use the 3 different runs or the 1 combined run.
2. This question may be a bit more difficult. In er-fMRI datasets, you specify stimulus onset by TR. The problem is that my TR and stim onset don't match. My stimuli are 4.25 s each and my TR is 2 s. This was chosen so that the image acquisition begins at various parts of the trail (as in Wheeler & Buckner, 2004). Is there a method for me to insert stim onset information in PLS? Essentially, I would need to insert stim onset in seconds rather than TR.
Thanks!
Erin
I am hoping to put a event-related fMRI dataset into PLS. I have two questions:
1. In pre-processing the data I performed motion correction and signal normalization in AFNI. I have this either for each of 3 runs, or concatenated into 1 run. When changing these into .nii files for PLS, is it best to use the 3 different runs or the 1 combined run.
2. This question may be a bit more difficult. In er-fMRI datasets, you specify stimulus onset by TR. The problem is that my TR and stim onset don't match. My stimuli are 4.25 s each and my TR is 2 s. This was chosen so that the image acquisition begins at various parts of the trail (as in Wheeler & Buckner, 2004). Is there a method for me to insert stim onset information in PLS? Essentially, I would need to insert stim onset in seconds rather than TR.
Thanks!
Erin
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Posted on 04/22/09 19:27:25
Number of posts: 291
Answer to Q1: I suggest that you use 3 different runs. This gives you an opportunity to choose "Merge Data Within Each Run" in the session window. Otherwise, I don't see any difference. However, in either case, please pay attention to the scan IDs that are going to be entered in the onset fields. i.e. if you decide to concatenate the runs together, you also have to concatenate the scan IDs together, and make sure that the scan files are in order. e.g. assuming that you have scan files from S001.img to S100.img in run1, and you have scan files from S001.img to S100.img in run2. If you concatenate the 2 runs, you must make them S0001.img to S0100.img for run1, and S1001.img to S1100.img for run2.
Answer to Q2: The answer is No. Our PLS program will only take an entire image file (1 scan, or 1 TR) as the smallest unit. Therefore, for 4.25s with TR=2s, I suggest that you enter 2 instead of 2.125. Even if you enter 2.125, the program will have to round them to the nearest integer. In onset filed, you must enter a number in the unit of TR instead of seconds.
Answer to Q2: The answer is No. Our PLS program will only take an entire image file (1 scan, or 1 TR) as the smallest unit. Therefore, for 4.25s with TR=2s, I suggest that you enter 2 instead of 2.125. Even if you enter 2.125, the program will have to round them to the nearest integer. In onset filed, you must enter a number in the unit of TR instead of seconds.
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