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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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Pages: 1234
Results 31 - 60 of 98
Hi, Daniel,
But I do not know the method to set AFNI_WEBBY_WAMI "NO". Does it mean that we set this in the resource or environment file? Any example for me?
J
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Juan
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AFNI Message Board
Hi, List experts,
I have a question in my mind for long time. If I want to do the ROI analysis for the fMRI data (say, block design experiment), can I also get the data point across time (i.e., 0-15s) as following example?
To illustration, when we let a person look at a stimulus, we will find a certain pattern of brain activation in the fusiform gyrus. At scan 1 the stimulus was presented;
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Juan
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AFNI Message Board
Hi, Daniel, Rick, and all,
I reported the same issue "AFNI crashing when using whereami" two times before, as well. To make it clear, I use SSH Shell to link my windows computer to the Linux server. When I used the old AFNI version, it is fine. The latest version never works with the "whereami" on my side.
J
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Juan
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AFNI Message Board
Thank you very very much, PT.
All your suggestion is very instructional and professional - I appreciate your help very much!!!
J
by
Juan
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AFNI Message Board
HI, AFNI experts,
I am thinking to use 3dNetCorr to do the whole brain network analysis (something like graph theoretical analysis) - is this possible? I do not understand the example of this command very well.
@ROI_Corr_Mat -ts s620_rest_r1+orig \
-roi SUMA/aparc.a2005s+aseg.nii \
-prefix s620_matrix_all_ROIs
My un
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Juan
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AFNI Message Board
Hi, List experts,
I was wondering whether we can directly get the information from the imaging files on how the fMRI data (i.e.,slices) were acquired. For instance, there are at least four types as following. These days I read papers and realize this question which is always in my mind.
Sequential Ascending: 1,2,3,4,5,6
Sequential Descending: 6,5,4,3,2,1
Interleaved Ascending: 1,4,2,5,3,
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Juan
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AFNI Message Board
Hi, Rick,
I have searched some old posts from you and other list users. I get to know that Dimon would extract the relevant information from the DICOM file and provide it to the to3d for the process. Given some issues, I tried to include two options (i.e., - assume_dicom_mosaic, -skip_outliers) to the Dimon command, but it does not work. To get clear what the exact process is, could you offer
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Juan
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AFNI Message Board
Hi, Rick,
Thanks so much for your prompt feedback.
Sorry, those are the dcm files (DICOM). They can be either functional or anatomical dcm files. for instance, in my folder" anatomical", there are many dcm files: image00005.dcm,image00006.dcm,image00007.dcm,image00008.dcm,image00009.dcm,image00010.dcm,....image00150.dcm,
I just tried using the command below,and got outputs: di
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Juan
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AFNI Message Board
For my data, I find some information
Private_0051_100e: 'Sag>Tra(2.1)' for one data set
Private_0051_100e: 'Sag> Cor (-2.7)>Tra(-0.0)' for another dataset.
I guess that they are some relevant to the z-axis or t-axis, but not confident. Any comments are much appreciated.
Juan
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Juan
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AFNI Message Board
Hi, List Experts,
Could you advise how I can use to3d to convert DICOM to nii format? I attempted to use the command.
to3d -prefix EPI_Sub1 -time: zt nz nt TR alt+z Input_DIC
I am NOT clear how to know whether my slices are in the order "z-axis first, then t-axis" or the contrary "t-axis first, then z-axis". Also, how to decide whether I should use alt+z, or alt
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Juan
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AFNI Message Board
Hi, List experts,
I attempted to do the "@Align_Centers" step to shift the center of both anatomical and functional data. However, I only get one output for the anatomical's. In detail, my script goes below (anatomical: Sub01_MP; functional :Sub01_EP)
@Align_Centers -base ../TT_N27+tlrc. \
-dset Sub01_MP+orig -child Sub01_EP
I only get the output, Sub01_MP_shft+orig.BRIK/
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Juan
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AFNI Message Board
Hi, Experts,
A quick question: When I do the ROI analysis, after I decide the ROIs (either anatomical based, or based on the activation coordinates) and make the masks, should I do the 3dfractionize step before I do the ROIstats?
Is the 3dfractionize step a must?
Thanks so much for your time,
J
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Juan
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AFNI Message Board
Hi List experts,
I am thinking to run a 3dttest++ with a covariate. I was puzzled as I do not know how to interpret the output. I have never used a covariate for a 3dttest++. Any good pointers for me? (It seems that in the 1d (common) t test, a covariate is impossible there. Am I right? )
I only have some basic thinking on 3dANCOVA (3dMEMA?). For instance, if the interaction of "main
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Juan
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AFNI Message Board
Hi, rick,
Thanks for letting me know your comments. I found that some people do the whole brain network analysis, also the MVPA, using the -stim_times_IM in the 3dDeconvolve. I tried it and found that by this way,we can produce a lot of data trials. This reminds me that some people claimed that a single trial data analysis (or, trial-by-trial analysis) is very powerful.
Clearly, this is di
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Juan
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AFNI Message Board
Hi, List experts,
I am attempting to do a single trial data analysis - some others call it trial-by-trial analysis. I know that in the 3dDeconvolve, we simply use -stim_times_IM for regressors of interest. However, for each event, we then have a lot of trials (i.e., data), then how should I do the 3dANOVA, or 3dttest?
For instance, in my experiment, there are three trial conditions: Post_e
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Juan
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AFNI Message Board
Hello, Rick and list experts,
I have now installed AFNI to my linux box. The version is "AFNI_16.2.16".
In the past years, I always use "Version AFNI_2011_12_21_1014". The "main difference" from my quick check is that once I open the new afni, it automatically shows the three images (axial, sagittal, and coronal). Previously, it only shows the former two image
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Juan
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AFNI Message Board
Hi Rick,
Do you have any suggestion for me if I want to install AFNI to NeuroDebian - I just installed an Oracle VM VirtualBox Manager to my Windows computer.
Thanks for your time,
Juan
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Juan
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AFNI Message Board
Hi, Rick,
Thanks for your message. I just checked two things below.
1) which tcsh
/bin/tcsh
So it means I have tcsh.
2) cat /proc/version
Linux version 2.6.32-504.16.2.el6.x86_64 (mockbuild@x86-028.build.eng.bos.redhat.com) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-9) (GCC) ) #1 SMP Tue Mar 10 17:01:00 EDT 2015
My question is how to contact RedHat to set up my Subscription Manag
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Juan
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AFNI Message Board
HI, List experts,
I still can not make the AFNI run. Anyone can help me?
Following the suggestion, from my home directory, I downloaded the file: wget
Then I used the script to execute it: tcsh @update.afni.binaries -package linux_openmp_64
Then echo command: echo 'set path = ( $path ~/abin )' >> .cshrc
All worked well. However, when I opened a new terminal and typ
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Juan
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AFNI Message Board
Hi, list Experts,
I used AFNI for a while, but now I try to install it to another computer, I meet a lot of problems. Can anyone advise me?
I follow the instruction here:
1)Install prerequisite packages.
sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc \
PyQt4 R-devel netpbm-progs gnome-tweak-tool ed \
libpng12
su
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Juan
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AFNI Message Board
HI Gang,
Woops, I arbitrarily used that only as an example. For instance, you also can assume that three conditions are as
"Larger Reward condition", "General Reward condition", and "Neutral".
Usually, people assume that there are difference between Large and General reward. My question is that if I now do not care the "Larger, or General reward"
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Juan
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AFNI Message Board
Thanks so much for your both. I have a further and special question for Bob.
Bob, I agree with you - that is very clear thinking. Suppose in my experiment (this is only for our discussion), I have three events: positive, negative and neutral. I can do the 3dDeconvolve in two ways, if I want to know the effect of emotion (i.e., positive and negative ones) vs. neutral. I define emotion as "
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Juan
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AFNI Message Board
HI Experts,
According to this webpage:
3dtttest program accepts datasets that are modified on input according to the following schemes: '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
With this in mind, I tried to do the t-test below, but it could not run (below is just a part of the script).
3dtttest++ -prefix ./Output_Cond/T_Test_Gain_Vs_Neutral_ShapeFi
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Juan
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AFNI Message Board
HI Jonathan,
I do not understand your message exactly. We do not want to include all classes. Let us have an example which I described before, say I only want to do the 1 vs.2 classifer. Can you confirm my 1D file below is correct or not?
line 1: 9999
line 2-41: 1
line 42-80: 2
line 81-125: 9999
line 126-166: 9999
line 167: 9999
or it should be
line 1: 9999
line 2-41: 1
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Juan
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AFNI Message Board
Dear Jonathan,
Thanks so much for your very patient reply. I have one further question.
"During training, 3dsvm will automatically train a binary classifier for each class combination and only select the data (sub-bricks) belonging to that class combination (e.g. for the 1-vs-2 classifier, the sub-bricks belonging to all other classes (class-3,class-4) as well as sub-bricks labeled wi
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Juan
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AFNI Message Board
My friend recently talked with me some questions on mvpa technique. He hopes to use 3dsvm for MVPA analysis but we both are puzzled with some options. I appreciate if anyone can offer advice here.
Our case is an event related fMRI study. Suppose that our experiment consists of 5 balanced runs. In each run of the experiment, there are four events: (1)House, (2)Building, (3)Threat Face, and (4)
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Juan
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AFNI Message Board
Gang,
Sorry I did not say it clear. My question is, when we do the 3dDeconvolve, we can use fixed-shape regression, such as BLOCK(d,p) method for each subject. Can I use its output for the ROI analysis. Let us have two 3dDeconvolve as examples below.
#1 shape fixed
3dDeconvolve -input rall_vr+orig \
-concat '1D: 0 108 216 324' \
-num_stimts 4 \
-stim_times 1 '1D: 17.5 | 1
by
Juan
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AFNI Message Board
Page 2 of 4
Pages: 1234