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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
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Dear AFNI experts,
I'm trying to do cluster-based multiple comparison correction for whole-brain-level p-values (saved in a sub-brick in AFNI file), and I was just wondering if 3dClustSim can be used for this purpose? Or is there another command I should use? Thanks!
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AFNI Message Board
Hi,
1). The command I'm using is:
3dfractionize -template anat+orig -input ROI+tlrc -warp tlrc_anat+tlrc -prefix ROI -clip 0.2 -preserve
2). I created a group-level ROI on the MNI space, and I was trying the align this single ROI back to each subject's original space. So I was just wondering if alignment will fail for this case?
Thanks!
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AFNI Message Board
Hi,
Yes that helped. Now the command is working. However the alignment looks pretty bad.. i.e., the ROI in the orig space looks misaligned. Is there a way to improve the alignment in this case? Thanks!
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AFNI Message Board
Dear AFNI experts,
I was trying to align ROIs in MNI152 space back to the orig space. It seems that 3dfractionize might be able to do it:
3dfractionize -template grid+orig -input data+tlrc \
-warp anat+tlrc -preserve -clip 0.2 \
-prefix new_data
However I got an error message saying: "Warp dataset doesn't contain a warp trans
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AFNI Message Board
Hi Rick,
Sorry for the multiple replies! But now I see another problem with your suggested method 1 (model the 0s stimulus with GAM or BLOCK(1.5,1), and model the 13s stimulus with 16 seconds of TENTs):
I was thinking about using TENT because I don't have any specific assumption about the shape of the HRFs. If I use GAM or BLOCK(1.5,1), then I feel like I'm ignoring what is happen
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AFNI Message Board
Hi Rick,
Thanks so much for your responses! I think that makes a lot of sense now!
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AFNI Message Board
Hi Rick,
Thanks for your response! Yes the variation is only during the ITIs. On each trial, a stimulus is presented at 0s for 0.5s, and after a brief 0.4s, a second stimulus is presented for another 0.5s. After that, no stimuli is presented until 13s, and this stimulus at 13s stays on the screen for 0 to 5s (this interval is determined by subject's response time). The ITI starts at 18s,
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AFNI Message Board
Hi Gang,
Yes, I'm analyzing the data at the individual subject level and I'm looking at the trial-by-trial data. I used to use raw BOLD signals in my data analysis. But since I used changing ITIs in my design, I would like to see if using beta weights will lead to better results. That's why I wanted to try the 'TENT' function.
Actually I'm just wondering if it
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AFNI Message Board
Here is some description of my experimental design:
I asked this question before and Gang suggested me to use a TENT function that lasts at least 25s. That's why I tried 26s at the beginning. I also tried 22s after that, this time 3dDeconvolve worked, but it took over half a day to complete the regression analysis... Is this a common problem for TENT function, or is it just because ther
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AFNI Message Board
I'm using the 'TENT' function to fit my data. I set the duration to 26s but the actual trial length varied from 22 to 28s. Here's my script:
3dDeconvolve -input epi_r??+orig.HEAD \
-polort 2 \
-float \
-allzero_OK \
-censor censor_epi_combined_2.1D \
-num_stimts 7 \
-stim_times_IM 1 epi_timing.txt
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AFNI Message Board
Thanks for the response! I think stim_times_IM is what I wanted. However, when I tried this command, I got the error:
FATAL ERROR: 3dDeconvolve dies: Insufficient data (2151) for estimating 2400 parameters
I think this error occurs because the duration of the regression function I'm using is longer than some of the trials. I tried using the '-allzero_OK' option as indicated in
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AFNI Message Board
Dear AFNI experts,
I'm trying to using 3dDeconvolve to regress on a trial-by-trial basis. In each run I have 12 trials (six conditions and two trials per condition). My question is, instead of using 12 separate stimulus timing files for each trial, is there a way in 3dDeconvolve to read in stimulus timings from a single timing file?
Thanks so much for your help in advance!
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AFNI Message Board
Hi Gang,
Thanks so much for your reply! Just want to clarify though: does it mean that I can reuse some of the time points from a next trial to model the HDR of a previous trial, since 25s is longer than some of the trials (18+4/6=22/24s)?
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AFNI Message Board
Hi Gang,
My experiment is kind of an event-related design. Two stimuli were presented during the 18s period. One was presented at 0s and another was presented at 13s. The inter-trial-interval varied in 4, 6, 8, and 10s. I want to model the entire process during the 18s, and that's why I want to use the 'TENT' function.
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AFNI Message Board
Dear AFNI experts,
I'm trying to use the 'TENT' function in 3dDeconvolve to fit my data. In my experiment, the trial length was always 18s, but the inter-trial-interval (ITI) varied in 4, 6, 8, or 10s. In this case, should I just model the 18s; or should I take the varied ITI into account? Also, since there's still stimulus-driven activity during the ITI, I was just wonderi
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AFNI Message Board
Dear AFNI experts,
I'm trying to merge two partial-overlapped ROIs (roi1.nii, roi2.nii, respectively). Specifically, I want to extract the shared voxels in the two ROIs and create a new ROI called roi3.nii. I know this might be quite easy to realize, but I'm just not sure if there is any existing function in AFNI that can do this.
Thanks for any help in advance!
Best,
Qing
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AFNI Message Board