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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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Hi Gang- Thanks for responding. I have a few ideas to try. When I find the solution, Ill post it here. -Jess
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defenderfer
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AFNI Message Board
Looks like I have autogzip set, but I dont see the compressor variable. I found out that removing -resid option from the anova allows it finish without error (including all subjects). I made a new post here with more information:
AFNI_ALWAYS_LOCK=YES
AFNI_AUTOGZIP=YES
AFNI_DEFAULT_IMSAVE=jpg
AFNI_DEFAULT_OPACITY=8
AFNI_DISP_SCROLLBARS=YES
AFNI_FLOATSCAN=YES
AFNI_GRAPH_FORCE_AUTO_SCALE=
by
defenderfer
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AFNI Message Board
Hi Gang, I found your replies to this post from several years ago. I am wondering if you could shed some light on my problem using 3dMVM -resid in the post below.
by
defenderfer
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AFNI Message Board
I posted a few days ago about a new problem Im encountering using 3dMVM. Rick Reynolds has been so kind to help troubleshoot (thank you, Rick), but unfortunately I am still having the same problem. I wanted to post a new topic with more information in hopes of increasing visibility to others that may have experience with my situation.
I have updated afni and r packages; when I run afni_system
by
defenderfer
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AFNI Message Board
Not that I am aware of. I didnt change any of the default settings. How would I check? So far I am able to run 8 participants with success and see an output file with results. Only thing I know to do, is continue adding participants back in, 2 at a time, to see when it fails.
by
defenderfer
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AFNI Message Board
I know, the activity monitor is a bit confusing. The "Memory" column reflects the total memory used (memory plus compressed memory). Technically, the amount of ram (of 32gb) being used at any given moment is at the bottom of the screen where it says "memory used". Sometimes it gets close to 32, but never seems to reach 32. And the "memory pressure" gauge doesnt show
by
defenderfer
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AFNI Message Board
After changing those two variables, running the anova, I still encountered the same error. A little over 30 minutes to get to slice 256 before seeing:
*** caught segfault ***
address 0x15f3e5f030, cause 'memory not mapped'
Traceback:
1: write.c.AFNI(filename, dset = brk, label = label, space = space, note = note, origin = origin, delta = delta, orient = orient, idcode
by
defenderfer
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AFNI Message Board
Thank you for responding. It took 18 minutes from slice 1 to 256 (which is a little faster than its finished in the past). I will try those variables. I am running 3dMVM with these options:
#!/bin/tcsh
3dMVM -mask clippedfullmask3.nii -prefix Accuracy_30 -jobs 1 \
-model 1 \
-resid /Users/jessicadefenderfer/Desktop/CV15_WAV72/ACC_30_RESID.nii \
-wsVars "oxy*acc*noiseType" \
-n
by
defenderfer
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AFNI Message Board
Hi again-
On the last slice of my 2x2x2 rm anova, I get this error:
*** caught segfault ***
address 0xfffffffd2524d030, cause 'memory not mapped'
Traceback:
1: write.c.AFNI(filename, dset = brk, label = label, space = space, note = note, origin = origin, delta = delta, orient = orient, idcode = idcode, defhead = defhead, verb = verb, maskinf = maskinf, scale = scal
by
defenderfer
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AFNI Message Board
nevermind, running @updateafnibinaries -d seems to have helped.
by
defenderfer
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AFNI Message Board
Im trying to run this 2x2x2 RManova with the residuals option; heres the top of my MVM file:
#!/bin/tcsh
3dMVM -mask clippedfullmask3.nii -prefix Accuracy -jobs 4 \
-model 1 \
-resid /Users/jessicadefenderfer/Desktop/CV15_WAV72/ACC_30_RESID.nii \
-wsVars "oxy*acc*noiseType" \
-num_glt 3 \
-gltLabel 1 OxyEff -gltCode 1 'oxy : 1*HbO -1*HbR' \
-gltLabel 2 AccEff -gltCo
by
defenderfer
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AFNI Message Board
Thanks for your reply. We start by averaging all 38 subject ROI masks into one composite mask:
3dMean -prefix allsubjectsmask.nii ~/Dropbox/fnirsauditoryproject2/processdata/p2process/S1001/viewer/Subject/1001_fullmask.nii
~/Dropbox/fnirsauditoryproject2/processdata/p2process/S1003/viewer/Subject/1003_fullmask.nii
~/Dropbox/fnirsauditoryproject2/processdata/p2process/S1004/viewer/Subject/100
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defenderfer
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AFNI Message Board
Their suggestion:
T-stat cluster statistic
The spatial (brain-space) covariance of the image based on the regularized Guass-Markov equation would be
CovBeta = inv(X'*X+lambda*I) * R
Where R is the channel-channel covariance and X is the forward model.
If your ROI/cluster is given by the contrast vector c = [0 0 0 1 1 1 1…] where the length of c is the number of voxels and is 1 i
by
defenderfer
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AFNI Message Board
We recently implemented an image-reconstruction method that uses AFNI tools to analyze our fNIRS data (validated in an fNIRS/fMRI paper: Wijeakumar et al. 2017). One reviewer for our recent manuscript provided feedback stating that we may be misusing the AFNI tools, so I'm here to get some feedback from the AFNI community. I'm not sure how much detail is necessary so I apologize for the
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defenderfer
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AFNI Message Board
Thank you for replying. I am going to put the surface projection on hold for now finish up the paper I'm working on. I will reach out to you once I get there!
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defenderfer
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AFNI Message Board
Hello
I am using afni programs to run 3d analyses on my fNIRS data. Now, I'm interested in projecting images onto a brain surface. Is this possible with just fNIRS data and afni tools, or must I have MRI structural data, too?
Thanks for any advice,
Jessica
by
defenderfer
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AFNI Message Board
Hello again, I'm trying to run a 2 x 3 ANOVA (using all between-subject factors) with 3dMVM, but I can't figure out how to designate gltlabels in the first few lines for the factor with three levels (NoiseLevel = quiet, enoise, noise). Based on info from the help page, I've tried the following:
#!/bin/tcsh
3dMVM -mask clippedfullmask.nii -prefix Noise -jobs 4 \
-model 1 \
-ws
by
defenderfer
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AFNI Message Board
Thanks again for replying. I'm sorry for the confusion- I only listed three because I have 38 subjects and didn't think it was necessary for the post. I've copied and pasted below the output with the final error message. I'm still missing something, and I cant get past that first GLT 1 error.
***** Summary information of data structure *****
38 subjects : S1001 S1003 S100
by
defenderfer
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AFNI Message Board
Thank you for your response. I used the command to fix the script. Now, it will run until it says "Reading input files: Done!" but quickly followed by this error message:
** Error:
Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct.
Warning message:
In summary.Anova.mlm(object$Anova, multivariate = FALSE) :
Singular error SSP matrix:
non-s
by
defenderfer
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AFNI Message Board
Thanks for any help. I am using a mac and tcsh shell.
My MVM file is titled MVM1.txt file using the command: tcsh -x MVM1.txt &. I receive this message:
3dMVM -prefix Accuracy -jobs 4
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Calls: process.MVM.opts
Execution halted
Everything else
by
defenderfer
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AFNI Message Board