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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 everyone,
After using "Clusterize" and "Rpt" buttons to generate the table of clusters, I notice that the XYZ coordinates and Z score obtained for the peak of each cluster in the table is different for the following 2 cases:
(1) Click "Jump" to move to the peak of a cluster, then observe the Z score value shown at "Thr = .. " on the bottom of the ma
by
dlhuynh
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AFNI Message Board
Thanks Gang for your answer.
Is the R^2 generated with -rout already adjusted for the number of regressors in the model, or do I have to calculate the adjusted R^2 manually?
Also, is the R^2 the mean of all voxel-wise R^2?
Duong
by
dlhuynh
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AFNI Message Board
Hi everyone,
I was wondering if there is an option in 3dDeconvolve or some other AFNI program that can calculate goodness of fit for GLM. For example, one can use TENT functions instead of a single BLOCK to model the response to a task, and would like to consider whether the TENTs or the BLOCK work better by comparing their goodness of fit. I haven't seen this is performed anywhere, and t
by
dlhuynh
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AFNI Message Board
Hi Gang,
For block designs, my understanding is we have to cast out 'rest' blocks and only keep and concatenate 'task' blocks in the time series when running GCA. Do we do the same for SEM? In case we have to do the same for SEM, there will be a lot of discontinuities in the ROIs' time series. I see that the 'model search' mode of 1dSEM can only be run with g
by
dlhuynh
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AFNI Message Board
Hello everyone,
When I run 1dSEM, I see a line saying "Connection directionality is from column to row" (column and row of Theta matrix). However, if I understand and remember things correctly, directionality is the other way around - row to column- for 1dGC or 1dSVAR. If this is true, is there any reason for the difference?
Thanks for your helps.
Duong
by
dlhuynh
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AFNI Message Board
Hi Gang,
Please see below.
cd /home/duong/share
3dMVM -prefix rm_mvm -jobs 8 -bsVars 1 -wsVars A*B*C -dataTable Subj A B C InputFile s1 c1 no r1 subrick13L_hs/ds_1_1_1+tlrc s1 c1 no r2 subrick13L_hs/ds_1_1_2+tlrc s1 c1 no r3 subrick13L_hs/ds_1_1_3+tlrc s1 c1 yes r1 subrick13L_hs/ds_1_2_1+tlrc s1 c1 yes r2 subrick13L_hs/ds_1_2_2+tlrc s1 c1 yes r3 subrick13L_hs/ds_1_2_3+tlrc s1 c2 no r1 subric
by
dlhuynh
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AFNI Message Board
Hi Gang et al.,
I am trying 3dMVM for a repeated-measures ANOVA where I have 3 within-subjects factors (A, B, C), and no between-subjects factors:
3dMVM - prefix rm_mvm \
- jobs 8 \
- bsVars 1 \
- wsVars 'A*B*C' \
- dataTable
Subj A B C InputFile \
.. .. .. .. ..
.. .. .. .. ..
by
dlhuynh
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AFNI Message Board
Hi everyone,
I understand that 3dClustSim is based on the spatial smoothness measured from the GLM residual term. In case one wants to run group analysis on some other kind of data, e.g. SVM weight maps, where the residual term does not exist, what is the suggested way to obtain an estimate of smoothness? Is it valid to apply the same smoothness (calculated from GLM)?
Thanks a lot.
Duong
by
dlhuynh
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AFNI Message Board
Thank you, Rick.
So I think I am good. From out.ss_review, my average TSNR is all >200 except for one subject (193).
By the way, what is the difference between the value reported in out.ss_review, and that computed by 3dBrickStat with -non-zero?
Duong
by
dlhuynh
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AFNI Message Board
Hi Rick,
It looks like the reason for low average TSNR is because of zero voxels. The 'full_mask' dataset contains '0' and '1' voxels, and TSNR = full_mask*signalMean/noiseStdev. And so when I used 3dBrickStat without the -non-zero option, it computed the mean across all zero and non-zero voxels.
With zero voxels excluded, my TSNR mean is much higher, in the rang
by
dlhuynh
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AFNI Message Board
Thanks for your reply, Rick.
We used TBV to keep track of motion in real-time in our experiment; I remember in general we had very little motion. We already excluded a few subjects that seemed to move too much.
I did a quick comparison of TSNR between a few "good" and "not so good" subjects. I saw a difference, the lowest was ~65, the highest ~89 (still kind of low compared
by
dlhuynh
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AFNI Message Board
Hi all,
Is the value of 200 from Robert's message the mean across the whole brain or just from some ROIs?
Our scanner parameters are roughly the same (3Tesla, voxel size 3x3, TR 2s, TE 30ms, flip angle 90 deg).
Our TSNR results are:
min=0 max=800-900 mean=70-90 stdev=110-180 (across the whole brain, runs and subjects)
The mean seems low. Do you think that is a problem?
Than
by
dlhuynh
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AFNI Message Board
Hi Rick,
Thanks a lot.
I managed to run the demo again with your suggestion for outputting the txt file but it didn't seem to work. The txt file was generated but I didn't see any data recorded and so the file remains at Zero bytes.
Another thing I don't understand is when running realtime_receiver.py with -verb 2, I don't see things that are supposed to be printed out wh
by
dlhuynh
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AFNI Message Board
Thank you Rick for your explanations.
There was no doubt that the real-time system will work. I simply asked my questions to understand better how it works and see if I can simply start from those demo programs (I think this is easiest because I have the data sent directly in real time from the scanner to the Mac already, which is similar to running the demo).
I understand from your answer that
by
dlhuynh
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AFNI Message Board
Hello all,
Following the instructions, I was able to run the real-time demo using programs under AFNI_data6/realtime_demos, but there are still a few things not clear to me.
My settings: - The three components (1) image monitor (using Dimon), (2) afni+ RT plugin, (3) real-time receiver are run on the same system (a Mac).
- I use Matlab installed on a separate PC to display feedback.
- D
by
dlhuynh
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AFNI Message Board
Hello all,
Following the instructions, I was able to run the real-time demo using programs under AFNI_data6/realtime_demos, but there are still a few things not clear to me.
My settings: - The three components (1) image monitor (using Dimon), (2) afni+ RT plugin, (3) real-time receiver are run on the same system (a Mac).
- I use Matlab installed on a separate PC to displa
by
dlhuynh
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AFNI Message Board
Thank you Rick for your comments/suggestions.
I have a few more questions.
1) You said the voxel level is always the uncorrected p-value, the
corrected p-values apply to the clusters. Does this apply to both FWE (p) and FDR (q)? I am wondering: if I use FDR (q under the slider bar) instead of FWE, do I need to set a limit for cluster size afterwards?
Maybe I am missing something impor
by
dlhuynh
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AFNI Message Board
Hello Afni experts,
I am kind of new to neuro-imaging and Afni, so please pardon these many basic questions.
I ran the proc script with both FDR and 3dClustSim and got the results attached to stats_REML. I am now looking at the stats_REML data in the GUI.
My questions:
1) Is the p value under slider bar corrected or uncorrected?
If I didn't run the Monte Carlo simulation with
by
dlhuynh
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AFNI Message Board
Hello,
I am trying to warp a cardinal anatomical dataset to an oblique functional dataset and obtain the transformation matrix:
3dwarp -card2oblique func+orig -verb -prefix obl_anat anat+orig
cat_matvec obl_anat+orig::WARPDRIVE_MATVEC_FOR_000000 > card2obl.1D
My question is: do I need to do any high- to low-resolution conversion before warping (using say 3dfractionize)?
Thanks a lot,
by
dlhuynh
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AFNI Message Board
Hi Rick,
I tried running 3dDeconvolve with 'jobs' set to 8 on my Mac Pro and Ubuntu 16.04 on my Desktop PC (8 cores). It was much faster on my Mac because "4 openMP" was used whereas only "1 openMP" was used in Ubuntu. What would be the reason?
I followed your instructions to install openMP for Ubuntu.
gcc version is 5.4.0
su -c 'yum install libgomp'
by
dlhuynh
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AFNI Message Board
Hello,
Below is part of the script I obtained using afni_proc.py. Since I wanted to check something in SPM after the despiking block, I need to convert the 3D+time dataset 'pb01.$subj.r$run.despike' back to individual 3D datasets, one for each TR, in the *.nii format.
What command would I use to do that?
Thanks a lot,
Duong
# ============================ auto block: tcat ====
by
dlhuynh
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AFNI Message Board
Hello,
I am wondering why I got the following error when running 1dplot.
==================
dhuynh% 1dplot outcount.r01.1D
++ 1dplot: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
++ Authored by: RWC et al.
Warning: Widget must be a VendorShell.
Error: attempt to add non-widget child "dsm" to parent "1dplot" which supports only widgets
===================
Th
by
dlhuynh
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AFNI Message Board
Hello. I used afni_proc.py to generate the script below.
I have a few questions:
(1) I wanted to remove the first 6 TRs, and so under the autoblock: tcat, you see '[6..179]' .
Moving a little further down, you see the 3dbucket command:
3dbucket -prefix vr_base pb02.$subj.r01.tshift+orig"[0]"
Question: should the sub-brick index
by
dlhuynh
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AFNI Message Board
Rick,
Thank you for your response. That was what caused the error.
I am pretty new to fMRI analysis; I just wanted to also include the baseline as though it were another active condition. This means that the boxcar function for the baseline condition will then also be convolved with an HRF before fitting to the data. This seems incorrect. However, since I suspect the subject might do some
by
dlhuynh
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AFNI Message Board
Hello AFNI experts,
I got the following "follows unknown arg" error when running afni_proc.py but could not figure out the reason. Could you please help.
(I am using AFNI 17.0.18 and afni_proc.py 5.13)
Thank you,
Duong
++++++++++++++++++++ SCRIPT +++++++++++++++++++++++++++++++++++++++++++++++++++++
#!/bin/tcsh -xef
# Include all sections, or some particular sections, of d
by
dlhuynh
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AFNI Message Board
Good morning!
I am using AFNI on my MacBook. When I right click on the brain images, I see a menu appear briefly and then disappear, and so I cannot select things on this menu. What would be the reason and how to fix it? I updated AFNI but the problem is still there.
Thank you for your help,
Duong
by
dlhuynh
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AFNI Message Board
Hi Daniel,
Thank you for your response.
So I am wondering what command should I use to extract the BRIK/HEAD files for each of the Brodmann areas 3 Left and 3 Right.
Sorry I am new to AFNI, and from this link ';, I found this line:
1 (sub-brick#) 83 (Value) Brodmann area 3
No separate values for the Left and Right areas.
Many thanks,
Duong
by
dlhuynh
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AFNI Message Board
Hello,
I am trying to locate the atlas datasets, i.e. TT_Daemon.Brodmannarea_*.BRIK/HEAD, for Brodmann areas 3 Left and Right to create masks.
I was told that they must be stored somewhere in the same directory as AFNI, but I couldn't find them.
Could anyone please help. I am new to AFNI.
Thanks,
Duong
by
dlhuynh
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AFNI Message Board