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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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Results 1 - 30 of 98
Hi, Taylor,
Thank you very very much - I have read it very carefully. Very informative and professional. Two further questions:
Quote---> this one says take the part of the input dset and make a mask wherever it has a value >3, and multiply that mask region by the actual value there (output type: short):
3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -e
by
Juan
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AFNI Message Board
Hi, Experts,
I previously created a mask with the method below, as a mask is required for the group analysis, e.g,. 3dttest++
3dmask_tool -input Sub*/*BrainMask+tlrc.HEAD \
-prefix mask_overlap.7 \
-frac 0.7
Sub*/*BrainMask+tlrc.HEAD stands for the brainmask from all subjects. All in all, this step generates a mask for the 3dttest++ and/or ANOVA2 analysis. Suppose my output is, Re
by
Juan
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AFNI Message Board
PT, thanks for your very professional comment. I agree with you. You are very funny - I like your sense of humor.
by
Juan
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AFNI Message Board
Dear, AFNI experts,
I am using our university server for my fMRI data analysis (through SSH Shell software). For now, when I log in to the server, the version is AFNI_2011_12_21_1014, which is definitely too old. In the server, there is the most recent version of AFNI installed there. Is there any way that I keep the current old version, but also use the current updated version of AFNI (I kn
by
Juan
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AFNI Message Board
Hi, AFNI experts,
When I ran the 3dDeconvolve script, I got some warning alarms. Example outputs are below. The "Safe_Event","Threat_Event", "Error", and "Feedback" are regressors. Are these alarms problematic?
Thank you very much.
J
*+ WARNING: Smallest FDR q [2 Safe_Event#0_Tstat] = 0.999749 ==> few true single voxel detections
++ Smallest F
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Juan
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AFNI Message Board
Hi, List experts,
I was thinking to report the activity wave for the region of my interest (ROI). I just found that in fact there is a function in the "Display": RowGraphs. According to the help, it says, "Rowgraphs lets you graph the voxel values from image rows". For instance, for my case, it shows two waves (one is in color, one is in black with the ROI point) -see the a
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Juan
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AFNI Message Board
Hi, Pt,
When I use the "echo $0", it returns "-sh", so not exactly a "bash" or "tcsh".
I use the command, "source ~/.bashrc", following with the "echo $DISPLAY", it returns ":0.0". So it is fine now, am I correct?
Thank you
btw, I tried the command "source ~/.cshrc", it shows quite a few rows, "-sh: setenv
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Juan
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AFNI Message Board
or does it mean that I need specially set the path for bashrc or cshrc, when I use the commands below?
echo "export DISPLAY=:0.0" >> ~/.bashrc
echo "setenv DISPLAY :0.0" >> ~/.cshrc
I have this question, as after I used them, I still got the alarm, "DISPLAY is not set. Please set your DISPLAY environment variable!". But I do not know how to set thi
by
Juan
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AFNI Message Board
Hi, Both,
Thank you both very much for your advice. I did try the command separately, also both at the same time (copy and paste, so I have not changed anything - is this fine?),
echo "export DISPLAY=:0.0" >> ~/.bashrc
echo "setenv DISPLAY :0.0" >> ~/.cshrc
But none of them worked - the same error alarm: Initializing: X11Error: Can't open display.
by
Juan
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AFNI Message Board
Dear experts,
My colleague and I are using SSH Shell and Xming to link a remote server, to run afni. It always worked very well in the past. However, it now can not work anymore. When I type "afni" and run it, it shows.
Initializing: X11Error: Can't open display:
++ AFNI is detached from terminal.
Definitely, my Xming is running normally here. So it is very strange to me
by
Juan
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AFNI Message Board
Dear Experts,
My colleague and I met a naive question on ROI analysis. Should we do the multiple-comparison correction, if so, how should we do?
Thank you very much,
Juan
by
Juan
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AFNI Message Board
Hi, Bob,
Could you confirm that the suggested way is correct? In the post, you suggested the command with a multiplication for conjunction analysis.
Suppose that F statistics are greater than 5, p =.01. Since you use the multiplication, the final conjunction threshold should be 0.01*0.01 =0.0001.
3dcalc -a 'stats+orig[7]' -b 'stats+orig[11]' -expr 'step(a-5)*step
by
Juan
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AFNI Message Board
Again, List experts,
I have read a paper for the conjunction analysis with AFNI, Emmorey et al., (2014), "How sensory motor systems impact the neural organization for language: direct contrasts between spoken and signed language" (Frontiers in psychology).
In this paper, (page 7), it reads, "We used false discovery rate correction for multiple comparisons to identify clust
by
Juan
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AFNI Message Board
Hi, PT,
Thanks for your clarification. I just tried and compared the two expressions below. It seems to me that the outputs are the same. Please let me know if I am wrong.
-expr 'a+2*b' \
-expr 'step(a)+2*step(b)' \
Thanks for your time,
J
by
Juan
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AFNI Message Board
Again, Daniel,
Perhaps I am using an old version of AFNI.
The command does not work with my computer. "3dcalc -a DSET1 -b DSET2 -expr 'a+2b' -prefix COMBO_1and2", the error alarm is below.
PARSER error 5: Expected an operator
A+2B
....#
** FATAL ERROR: illegal expression!
but it works if I change the -expr 'a+2b' to -expr 'step(a
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Juan
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AFNI Message Board
Hi, PT,
Thanks a lot for your prompt reply. Two further questions.
1), why is the calculation expression is 'a+2b", rather than 'a+b"? Does it mean that your 'a+2b" stands for DSET1, DSET2, and both in DSET1 and DSET2? I assume that 'a+b" is equal to show the value of voxels from DSET1 and DSET2. Am I correct? How to obtain the both in DSET1 and DSE
by
Juan
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AFNI Message Board
Dear List experts,
I have a quick question. How can we overlay different results to the mask, using AFNI? I read a paper - the authors used this method, but with FSL (perhaps fslview tool). In that paper plot, there are two conditions displayed in the same task: affective display, informative display. They also showed the conjunction display with the same mask. The example display is attache
by
Juan
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AFNI Message Board
Thanks so much, Daniel.But do you have any suggestion to use that VMPFC (In that post, you introduce the paper and we can download the mask, but it includes a lot of small masks of VMPFC). They are MNC formatted files, but AFNI can read it. Does it mean that if I want to only use the general VMPFC, I need first combine all of them? Thanks so much!!!
by
Juan
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AFNI Message Board
It seems that I need first resize and make them same in the size...
by
Juan
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AFNI Message Board
Hi, List experts,
I had problems during the ROI combination, but I do not know how to understand the error alarms below. Is that I have problems with the ROIs themselves or anything else?
Thanks so much,
Juan
$ 3dcalc -a MPFC.nii -b VMPFC.nii -expr '(a+b)' -prefix PFC.nii
++ 3dcalc: AFNI version=AFNI_16.3.13 (Nov 23 2016) [64-bit]
++ Authored by: A cast of thousands
**
by
Juan
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AFNI Message Board
Hi, Bob,
Could you advise me how to use the cluster-level corrected alpha of .05 to report the group results now? Or could you let me know your new paper - does it address this issue? Is this method still valid: " the alpha-level for voxelwise statistical analysis was determined by simulations using the 3dClustSim program of the AFNI toolkit. For these simulations, the smoothness of the d
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Juan
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AFNI Message Board
Thank you very much, PT!!! Now all are really clear to me.
Cheers,
j
by
Juan
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AFNI Message Board
Hi, AFNI experts,
Here I have a quick question on ROI analysis. According to my understanding, there are at least threee ways to do the ROI analysis. 1). We can get the ROI coordinates (x,y,z) from the fMRI data analysis, say, a t-test (Reward vs. noreward). Let us have the left side Anterior Insula as an example: Left AntInsula, (-28, 20, -1); 2). Based on the classic literature or meta-analys
by
Juan
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AFNI Message Board
Hi, Pt,
One more question:
On your example script, 1) the input for "-inset" (in your example, it is "REST_in_DWI.nii.gz "). As I said before, I assume that this script can be for both rest-state fMRI and task based fMRI. With regard to the input file, I do not exactly know your meaning of the 4D data. I think it should be the output from the standardized preprocessing
by
Juan
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AFNI Message Board
Thank you very much, Gang,
So it means that we can use TENT/TENTzero, CSPLIN/CSPLINzero for block designed datasets. I was wrongly thinking that we only can use them for the event-related design.
J
by
Juan
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AFNI Message Board
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Pages: 1234