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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
History of AFNI updates
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Thank you for the response! I will try that. Can I ask, why TENTzero instead of TENT?
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wped
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AFNI Message Board
Blocks were separated by 20 s.
I attempted 3dsynthesize on one of my subjects. I added the cbucket option my 3dDeconvolve, with conditions modeled using the BLOCK function. I then ran:
3dSynthesize -cbucket ${results}/all_betas+orig \
-matrix ${results}/X.xmat.1D -select 12 -cenfill nbhr -prefix ${results}/PredictableNegative_timeseries.nii.gz
with the 12 in the -select option bein
by
wped
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AFNI Message Board
I am modeling a task with a mixed block event-related design. It has four block conditions (negative vs. neutral images with predictable vs. unpredictable presentation timings). Blocks are 91 s long, and there are two blocks of each condition type. I modeled these blocks with the BLOCK function, and found some interesting differences within a couple of ROIs.
Now I would like to graph the ti
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wped
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AFNI Message Board
I've found that when I plot the condition means for these two models side by side (with trial collapsed, so they can be compared directly), most of the mean estimates are fairly similar. Because of this, I am guessing there is nothing wrong with the way I used 3dLSS, but rather that the different ways of modelling the data caused relatively small differences in how the means were estimated,
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wped
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AFNI Message Board
Hi Afni Experts,
I am analyzing a study looking at the amygdala and hippocampus response to novel and repeated stimuli (with two other factors, emotional vs. neutral and humans vs. scenes). I first ran a pretty standard proc.py using a tent function to model the different conditions and extracted the resulting data (tents 2-5) for amygdala and hippocampus ROIs made through freesurfer. Here i
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wped
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AFNI Message Board
Hi Rick,
That is a very helpful point, I will have to take that idea and run with it and see how much space that can save us.
Thank you!
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wped
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AFNI Message Board
Hi AFNI experts,
Our lab is going to run a high resolution 7T study soon. We have data from multiple 3T studies already, and data storage is already a taxing issue. Since I am assuming the high resolution files will be much larger, I was wondering if anyone had any tips for efficient data management?
Thanks
Walker
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wped
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AFNI Message Board
Hey Rick,
I am using functional data with this. I processed it through proc.py, and the defaults on that appear to be smoothwm for surfA and pial for surfB, so it sounds like the slow_surf_clustsim.py defaults are fine, I just need to change my SurfClust surf_A option to smoothwm.
Thanks for your help!
Walker
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wped
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AFNI Message Board
Hi Rick,
Thanks for the reply, sounds good.
Quick follow up question - when I use -show_default_uvars I see that it has surfB as pial. What does surfB mean?
Thank you,
Walker
by
wped
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AFNI Message Board
It sounds like at least a couple of people on here are using the pial surface in their surfclust commands. However, I've noticed the interactive clustering in suma uses the smoothed wm surface. This seems to make a significant difference for the size that the clusters are estimated at, thus changing which ones get kept.
I'm not seeing a slow_surf_clustsim.py option that specifies w
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wped
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AFNI Message Board
Ziad suggested that I may be trying to blur to a smoothness that is very close to the smoothness already in my data. I increased my blur from 4 to 5, and that did the trick.
Thanks for the help!
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wped
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AFNI Message Board
Hi Rick,
My proc.py finished over night, and it looks like this problem is happening with about 30% of my subjects. I don't know if that points to this being a problem with my proc.py command or something...
In any case, I can't see anything visually wrong with the pb03.*.lh.r01.surf.niml.dset files for those subjects. Is there anything else I can do to check these files?
If
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wped
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AFNI Message Board
Hi Rick,
The surf.smooth.params.1D file reads:
#Final smoothing parameters via master:
#Niter Sigma OutputFWHM
0 1.0395 -1.000
I have emailed you the proc.py output.
Thank you!
by
wped
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AFNI Message Board
I am running a surface analysis using proc.py. I've got a script that is currently running, and several subjects have finish successfully, but I am getting an error for one subject:
Error SUMA_SurfSmooth_ParseInput:
Unexpected combo: fwhm -1.000000, tfwhm -1.000000, sigma 1.039500
I don't see anything specifically weird about this subject. I've previously used proc.py on i
by
wped
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AFNI Message Board