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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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Thanks a lot Peter and Rick! Since the behavioral regressor will vary across subjects, it could become collinear with some other regressor in the design and I would like AFNI to abort in such a scenario. So, -allzero_OK option seems more appealing to me, unless there is a strong reason to not use it.
Regards,
Gaurav
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gauravm
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AFNI Message Board
Hi all,
I have some behavioral regressors in .1D files that I want to include in my analysis. However, for some subjects these regressors can be zeros. Is there a way to pass the '-allzero_OK' option to 3dDeconvolve from afni_proc.py command? I would prefer to not modify the proc script generated by afni_proc.py.
Thanks a lot,
Gaurav
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gauravm
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AFNI Message Board
Hello Rick,
I have a similar question. I have a regressor in the form of a 1D file (a behavior measure). I want to convolve it with the HRF and use the result as the final regressor. But I want to do it at the afni_proc.py level. I imagine there must be a simple way to do it but have not found it. Any hints?
Thanks,
Gaurav
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gauravm
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AFNI Message Board
Dear all,
I installed AFNI on a new machine and then installed R via the command
rPkgsInstall -pkgs ALL
Then I checked the R installation via
rPkgsInstall -pkgs ALL -check
I get the following warnings:
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
I tried to check the FAQs but there are no FAQs, perhap
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gauravm
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AFNI Message Board
Hello Y'all,
The Afni manual suggests bandpass filtering the timeseries before running connectivity analysis. I was wondering about the ringing artefact that results from bandpass filtering. Can someone tell me its effects on the connectivity analysis?
Thanks and regards,
Gaurav
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gauravm
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AFNI Message Board
> 2. Contrast maps. I have two conditions in the experiment and I want to contrast the brain
> activation across them. What should be the appropriate extent threshold to apply to the
> contrast? Should I first subtract the residual of one condition from the other's, then use that
> difference timeseries as input to FWHMx and proceed as usual?
->Even though not ideal, the
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gauravm
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AFNI Message Board
Hello Everyone,
I think I understand how the extent threshold is determined for a simple task-based voxelwise analysis. I find out the smoothness of the residual timeseries, feed that to the monte carlo simulation of noise done by 3dClustSim, which gives the extent thresholds at various uncorrected p-values to get the desired FWER. Correct me if I am wrong.
I need to know what is the way to
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gauravm
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AFNI Message Board
Hi Rick,
The orientation is fine, I actually want to rotate it because I'm using a custom built matlab code to do some spinal analysis. But matlab is loading the images pi/2 rotated and the easiest fix is to rotate the original image by pi/2. But thanks for looking out for me!
Best,
Gaurav
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gauravm
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AFNI Message Board
Hi Dan,
I tried -zpad from 20 to 100 in increments of 10. The cut corners gradually come back with increasing -zpad. Turned out that I need a minimum of 70 to completely recover the corners.
I also tried -cubic and other interpolations but those also need a zpad of 70.
One thing I failed to mention thinking it to be not important is that the dimensions of the volume are 192x192x8 voxels (
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gauravm
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AFNI Message Board
Sorry, -zpad 200 did it for me, I guess I hadn't loaded to correct file to view earlier. Thanks a lot Dan!
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gauravm
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AFNI Message Board
Hi Dan,
I had tried the -Fourier option, it didn't help. I hadn't tried zpadding extensively though. Now I did -zpad 20 and 200; neither solved the problem for me. I still have these thick slits which cut off the two corners. Would you like me to upload the data?
Best,
Gaurav
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gauravm
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AFNI Message Board
Dear all,
I am trying to rotate an epi series using 3drotate. The command I am using is reasonable:
3drotate -rotate -90L 0A 0I -prefix L-90.nii SPINAL-002_WIP_TSE_BOLD.nii
The output image is rotated but it has a couple of slits which cut off the top left and bottom right corners of the image. I tried to attach a snapshot of the output but can't see it attached with the message. I'l
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gauravm
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AFNI Message Board
Hi Rick and Nick,
Thanks a lot for your responses, I will just edit it.
To answer your question Nick, it happened to only one functional scan, the preceding and succeeding scans have TR=2.5 and all scans were run with identical parameters.
Thanks again,
Gaurav
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gauravm
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AFNI Message Board
Dear all,
Even though I specify TR=2.5 s during acquisition, the value of TR happens to be 2.499 s for one of my functional scans. I can see that with 3dinfo. It would not be a problem if all other scans also had TR=2.499 but since they have TR=2.5, afni_proc.py is throwing the following error and bailing out
** TR of 2.499 != run #1 TR 2.5
---------------------------------------------------
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gauravm
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AFNI Message Board
Hi Rick,
Sorry to revive this old thread. I need to know the exactly how the percent signal change (PSC) values in iresp file are calculated.
When using the tent function, what does 3dDeconvolve use as the baseline - the overall average of the timeseries or the average signal during the "rest" TRs (as inferred from the stim file)?
Thanks,
Gaurav
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gauravm
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AFNI Message Board
Hi Rick,
I did what you suggested and found that the two methods (MASKAVE and VECTORS using the same mask) give almost identical results, but not identical. I can live with that but I expected the results to be identical.
Thanks a lot for your help!
Gaurav
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gauravm
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AFNI Message Board
Hi Rick,
Sorry, I meant that I align the anatomy to the SUIT template, save the transformation map and apply that to the stats file to "align" it to the SUIT template. I took a shortcut in explaining that and used the word align loosely.
The cerebella masks will vary only after I back transform them to subject space.
The entire procedure is as follows:
1. Regular afni_proc.py w
by
gauravm
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AFNI Message Board
Dear all,
I want to use 3dGroupInCorr for connectivity analysis but I want to supply my own timeseries as seed. The first question is how. I looked up the batch option in 3dGroupInCorr program help and found a METHOD called VECTORS which allows one to specify a timeseries in a .1D file but there is a warning there that reads:
** N.B.: This method has not yet been tested!
Is there any updat
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gauravm
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AFNI Message Board
Forgot to mention - even though the anatomy is at 2x2x2 resolution in standard space, the stats is still at 3x3x3 resolution in standard space. So, doing MC simulations at 3x3x3 is appropriate even at the group level.
by
gauravm
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AFNI Message Board
Hi David,
Thanks a lot for bringing up the point about a principled approach for determining the combination of p-threshold and extent threshold for achieving a desired alpha value (familywise error rate). Multiple combinations of p-threshold and extent threshold give the same alpha value. Conjunction analyses (where you try to find overlap of activity across conditions in order to determine mul
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gauravm
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AFNI Message Board
Thanks a lot Rick, its a relief to know that.
Best,
Gaurav
by
gauravm
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AFNI Message Board
Dear all,
I have a single-subbrick stats file in nifti format with float datum type. When I use 3dcopy to convert it to .BRIK format, I get the following warning:
WARNING: file wcmstats.03.nii: corrected 2143 float errors
I was wondering what this can be about.
How do I get the wcmstats.03.nii file? I convert the stats.03+orig.BRIK file (that I get from afni_proc.py) to nifti using
3dAFNI
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gauravm
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AFNI Message Board
Dear all,
I am using the TENT function and -iresp option in 3Ddeconvolve. I am scaling the data before running 3Ddeconvolve.
Can someone please confirm that the contents of the iresp file are the beta values of the fitted TENT function and that these beta values are directly interpretable as the percent signal changes at their individual time points?
This will be great help.
Thanks a lot
by
gauravm
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AFNI Message Board
Dear all,
I have to create ROIs for each individual. The idea being that people are different so they don't show activity in exactly the same spot. Is there a way by which I could do the following in a script:
1. Identify the peak voxel of a cluster, save its coordinates
2. Using those coordinates as the center and a given radius, insert a sphere in a blank dataset and save the dataset.
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gauravm
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AFNI Message Board
Hi Rick and everyone,
I guess this message got buried under others. Hence, reposting for your consideration.
Best,
Gaurav
by
gauravm
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AFNI Message Board
Hi Rick,
I had imagined that the -cdep option would make more sense because the brain voxels are not independent due to spatial correlation. Could you please elaborate on why should we use -cind and not -cdep?
The FDR map generated by 3dDeconvolve and the FDR map obtained by running the stats file through 3dFDR are identical when I use the -cind option but not identical when I use the -cdep o
by
gauravm
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AFNI Message Board
It seems to me that when afni_proc.py refits FDR info in the stats file, it uses the -cind option of 3dFDR. Any thoughts please?
Thanks and regards,
Gaurav
by
gauravm
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AFNI Message Board
Dear all,
When I use 3dFDR with the -cdep option on my stats file, it converts the t-stats (ranged from -5 to 8) to Z-scores ranged from 0 to 0.6, which means I have to reject every single voxel. However, if I use the -cind option, the output Z-scores range from 0 to 2.1, which is much more palatable.
I would like to know more about which option is better to use and why. I had imagined that t
by
gauravm
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AFNI Message Board
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