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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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Howdy-
Thank you for your reply, it helps me a lot. Actually, I noticed that the color in high-level journals is often low saturation and soft. However, the colorbars provided by afni have a high saturation, which makes the image dazzling. So I extracted the color of high-level journals and customized the color bar with low saturation. And I think it may look better to make such a picture. If af
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hjr61547
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AFNI Message Board
Hello you all,
I want to create a new colormap based on my RGB fIle. And I want to add the new colormap to the afni gui. So I can use it when I open the afni and invoke the colormap. But how to do this?
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hjr61547
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AFNI Message Board
Hi,
Thank you so much for your reply. Actually, I created some masks as my ROI. And I give the masks different values. Then I use 3dcalc to compose these masks.like:3dcalc -a AN.nii -b VN.nii -c DMN.nii -d ECN.nii -expr 'a+b+c+d' -prefix Network.nii. The final result is the first picture.
Now what I want to do is add the edges for the mask. Then I will use SUMA to get a surfac
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hjr61547
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AFNI Message Board
I create a mask as ROI, now I want to add the edge for the mask. How can I do it?
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hjr61547
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AFNI Message Board
When I do the preprocessing of a child (3 years old), the program always makes mistakes in registering to the standard space.I found the template on the Internet, not AFNI's.
problem: 3dNwarpApply -nwarp "./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D" -master ./base.nii -source /media/hjr/zlw/SCNU_ASD/test/1110083/1110083.results/T1+orig -prefix ./T1.aw.nii
++ 3dNwarpApply: AFNI
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hjr61547
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AFNI Message Board
Hi, AFNI experts
Is AFNI capable to generate a simulated fMRI data? For example, I want to create a fake fMRI data which consists of 300 TRs. Which program is able to achieve this aim?
Thanks.
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hjr61547
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AFNI Message Board
Hello, afni experts
When I used 3dMVM to conduct a ANOVA analysis, an error message showed up:
[1] "Great, test run passed at voxel (55, 42, 31)!"
Error: $ operator is invalid for atomic vectors
Execution halted
My intention is to calculate the main effect of sleep stage (Wakefullness, N2, N3). As some sleep stage did not showed up in some subjects, we enlarge the data sampl
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hjr61547
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AFNI Message Board
Dear AFNI experts,
When I was used LONG form in 3dttest++, a fatal error "Option -setA: can't open dataset 'subj01.SN.EC.z+tlrc' " always comes up. But, I examined the name of my dataset again, there were no mistakes. Each dataset only had one sub-brick which contained fisher transformed z value on each voxel. Also, the label of each dataset in covariance table is the
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hjr61547
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AFNI Message Board
Hello AFNI experts,
In SPM, there is a dynamic casual model function.But I am not familiar with SPM, can I do the same thing in AFNI? If AFNI can calculate dynamic casual model ,what program should I use?
Thanks a lot!
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hjr61547
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AFNI Message Board
Hi,AFNi experts,
When I have put an ROI mask on anatomical image as overlap, how can I put another mask on it and make these two overlap in different color?
Thanks for your help
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hjr61547
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AFNI Message Board
But seed data needs 3D+time dataset. 1D file can't use as a seed data.
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hjr61547
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AFNI Message Board
Hi, AFNI experts,
I want to use a ROI as seed to correlate with all other voxels. Now I have got a ROI mask, but how can I use this ROI mask to create a seed dataset?
Thanks all
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hjr61547
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AFNI Message Board
Hi, AFNI experts,
When I use paired 3dtest++ to analyse my group data between eyes open(EO) and eyes closed(EC) which is within subject, I want to add head motion as covariates. Therefore, I calculate averaged motion across all TRs in each subject's condition(EC and EO). And I got 6 number for each subject's condition,represented for 6 motion parametric(roll, pitch ,yaw,ds ,dl,dp).Th
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hjr61547
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AFNI Message Board
Thanks you!
Aafter change the line you wrote, the 3dMVM works very well
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hjr61547
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AFNI Message Board
Thanks again!
But after I change the line, ti still occurs error.Is it my R problem?
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hjr61547
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AFNI Message Board
Thanks for your advice! But after changing the line as you said, it still occur the same error.
Read 305 items
Error in outList[[1]][] : subscript out of bounds
Calls: process.MVM.opts -> gl_Constr
Execution halted
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hjr61547
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AFNI Message Board
Hi,every AFNI experts
When I used 3dMVM to test my data, it occur this error message:
Read 305 items
Error in outList[[1]][] : subscript out of bounds
Calls: process.MVM.opts -> gl_Constr
Execution halted
I want to to do a ttest between 2 conditon(eyes open and eyes closed within subject), but thess data from two dataset(scan1,scan2).So I wrote a code like:
3dMVM -prefix ECvEO -jobs
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hjr61547
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AFNI Message Board
Hi, every AFNI expert
In generally, resting-state BOLD signal range in 0.01-0.1. But when I see afni_proc.py newest example 11b for resting state, I notice there is no bandpass anymore. Why is that? Can I band pass later when I finish example 11b?
In case of reminding others who are also interesting in this question, I copy the example 11b from afni_proc.py
afni_proc.py -
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hjr61547
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AFNI Message Board
My apology, I mean Matlab Library can't be downloaded any longer in AFNI website.Where can I get this toolbox ?
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hjr61547
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AFNI Message Board
Hi,AFNI experts
Recently I need to pocess my afni data in matlab,but I have found Matlab Library no longer useful. Is there another way I can read, write, and process AFNI datasets in Matlab?
Thanks
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hjr61547
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AFNI Message Board
Hi, everyone.
After I use maskave to get a 1D. file from ROI, I need to find out the values which are stronger than 80% of the rest and mark the 20% stronger value as 1 and the rest as 0 in another file for censor in 3Ddeconvolve. Which program should I use?
Thanks all.
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hjr61547
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AFNI Message Board
Hi,everyone
I want to calculate the variation of dataset. I have used 3dTstat -stdev, but the result doesn't seem well. So I want to try the latter volume minus the volume, for example,sub-brick#2-#1,#3-#2,#4-#3.......In this case,what program should I use? If no program can do this , can I use 3dTcat to select every 2 sub-brick by using the selection list,like red+orig[0..$(2)] and blue+
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hjr61547
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AFNI Message Board
Hi,everyone
How can I use AFNI to do the K-means clustering? Because I want to identify different connectivity patterns.
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hjr61547
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AFNI Message Board
Hi, everyone
I am hoping to make a mask of all regions of TT_Daemon for 3dTcorrmap. Because I want to save time in processing and get more specific information on TT regions.
Can I do this mask in whereami? Or I need to put all these regions together using 3dTcat?
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hjr61547
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AFNI Message Board
3dfim+ - 6 years ago
Hello,
I was hoping to use 3dfim+ to calculate the cross-correlation of a alpha power time series with the measured FMRI time series for each voxel. But an error occur:Input ideal time series file 'EO_alpha_ps_conv_HRF_ts_normalized.txt' is too short. I am sure my FMRI time series has 187 data points and my alpha time series also has 187 data points.
I am wondering if txt. is not
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hjr61547
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AFNI Message Board
Thanks for your answer.
The order actually appear disorder.How can I fix this problem?
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hjr61547
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AFNI Message Board
Thanks for your help.
But when I use your script, it occur such message:set nums = ( `count -digits 1 1 186` ) bash: syntax error near unexpected token `('
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hjr61547
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AFNI Message Board
3dTcat - 6 years ago
Hello,
I was hoping to concatenate 186 3D+time datasets into one big 3D+time dataset. Their names are "Z_EC_thalamus_1" "Z_EC_thalamus_2" "Z_EC_thalamus_3" "Z_EC_thalamus_4" "Z_EC_thalamus_5" ...... How can I use 3dTcat to simply concatenate them? I don't want to print all 186 names in one command.
Thanks all!
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hjr61547
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AFNI Message Board
Alpha power time series (stim_file 1) is a time series with a value at each time point that should be convolved with HRF. After checking the help in 3Ddecnonvolve, I prefer WAV as my interested function.
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hjr61547
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AFNI Message Board
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