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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 1 - 30 of 94
Dear afni experts and users
I am trying to preprocess my fMRI data. Is there any code in afni that i can use to test whether my data were smoothed, e.g., FWHM=6 mm?
Thanks.
best.
rujing
by
charujing123
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AFNI Message Board
Hi
The ALFF could provide summary amplitude of e.g., 0.01~0.1hz. How to calculate power spectrum for each frequency?
Thanks
rujing
by
charujing123
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AFNI Message Board
Hi Gang
Thanks for your reply. I tried -model "CiJi*QainHou*Contrast3"\, and same error remains:
=================
sub52 24 0
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
Reading input files: Done!
Range of input data: [0.000, 1.810]
If the program hangs here for more than, for example
by
charujing123
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AFNI Message Board
Hi Gang
Thanks, Now I have intalled "nlme", "lme4", "phia", "snow" (checking them in the R with installed.packages()).
However, new error comes when trying 3dLME:
============
Briefly, it is "Error in if (ii < dimx) ii <- ii + 1 else if (jj < dimy) { :
missing value where TRUE/FALSE needed
Execution halted"
============
The scr
by
charujing123
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AFNI Message Board
Dear AFNI experts
I have also a 'phia' install problems:
The OS is CentOS Linux release 7.9.2009 (Core);
The R is R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
# ./rPkgsInstall -pkgs 'phia' -update -site ';
Installing package into ‘/roo
by
charujing123
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AFNI Message Board
Dear AFNI experts
I have also a 'phia' install problems:
The OS is CentOS Linux release 7.9.2009 (Core);
The R is R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
# ./rPkgsInstall -pkgs 'phia' -update -site ';
Installing package into ‘/roo
by
charujing123
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AFNI Message Board
Dear AFNI experts and users,
I used multiple voxel pattern analysis to decode conditions from the OFC. But, one reviewer commented this:
====
It is a bit unclear whether multiple voxel pattern analysis will have sufficient signal-to-noise given high susceptibility OFC. The authors should clarify that they have sufficient signal to measure.
====
So how can I test and measure whether the OFC
by
charujing123
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AFNI Message Board
Hi Gang,
Besides the Z and SE, how to measure the 95% confidence interval?
Thanks
Rujing
by
charujing123
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Each post hoc inference through -gltCode gives you
> two values per voxel: effect estimate and
> t-statistic. You can directly obtain the standard
> error (dividing effect estimate by t-statistic).
> Once you have the standard error, I think there is
> a way to plot the result at the voxel level
> a
by
charujing123
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AFNI Message Board
Hi Gang,
> The proper way to do this is to add two more
> specifications:
>
> -gltCode ... 'CiJi : 1*anode QainHou : 1*after
> Contrast3 : 1*now' \
> -gltCode .. 'CiJi : 1*anode QainHou : 1*before
> Contrast3 : 1*now' \
>
> Then combining with the original one -gltCode 6
> 'CiJi : 1*anode QainHou : 1*after -1*before
> Contras
by
charujing123
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AFNI Message Board
Hi Gang,
Nope, the "anode" did not mean a voxel or an anatomically or statistically defined region. The "anode" is one condition of within-subject variable "CiJi". Similarly, the "QainHou" (two level: after vs before) and the "Contrast3" (two level: now vs notnow) variables are within-subject variables.
In the current LME model, effect of this
by
charujing123
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AFNI Message Board
Dear AFNI experts and users,
After running the 3dLME as below, I find a significant result in "-gltLabel 8 after_before_in_anode_now_or_notnow". Does anyone know how to extract the effect of 'after-before' in anode for each individual in the current model? Then I can use them for scatter plot.
Thanks.
All the best.
Rujing
3dLME -prefix Example3 -jobs 1 \
by
charujing123
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AFNI Message Board
Hi Gang,
Thanks very much for your reply. I have two more questions:
question1:
I am also interested in main effect of conditions and in comparing condition 1 among the subjects in group 1 and condition 3 among subjects in group 2. Based on this, is 3dLME better?
question2:
I would like to know where I could find voxel sizes, then I can use them to set the Clustersize in the AFNI GUI (m
by
charujing123
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AFNI Message Board
Dear Gang,
Thanks for your reply and help.
There were 10 conditions: thegood othergood, reject accept, healthy tasty, generous selfish, forage engage. For each subject, there were only two conditions, e.g., 12120 only has generous and selfish, and does not have other eight conditions.
The research questions is whether there are any differences between contrasts. Could this be called main e
by
charujing123
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AFNI Message Board
Dear Gang, AFNI experts and users
I have 5 groups subjects. Condition1 and condition 2 were performed for each subject in group 1. Condition 3 and 4 for group 2. Condition 5 and 6 for group 3....
======
Subj contrast roi InputFile \
12120 generous roi_25 beta_12120_generous_x_roi_25_allrun+tlrc \
12120 generous roi_26 beta_12120_generous_x_roi_26_allrun+
by
charujing123
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AFNI Message Board
Hi AFNI experts and users,
When trying to preprocess task fMRI data in the human connectome, I encountered a problem. There were two runs for each task. The one run was acquired with right-to-left phase encoding, and a second run with left-to-right phase encoding (in-plane FOV rotation obtained by inverting both the RO and PE gradient polarity). So, how to combine two phase encoding runs in t
by
charujing123
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AFNI Message Board
Hi rick
I want to perform the signal-noise-ratio. Could i use the 3dTstat with -tsnr on the perprocessed data (after normalized, motion corrected, detrend...)?
Thanks.
rujing
by
charujing123
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AFNI Message Board
Hi
Using stim_times_IM and TENT(0,8,5) in the 3dDeconvolve, I got output with 432 sub-bricks. My question is the neighbor brick means neighbor stimulus (in stim_times_IM) or neighbor TRs (in TENT)?
Thanks
rujing zha
by
charujing123
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AFNI Message Board
Hi Paul
Thanks for your reply. I will check that phase in Tortoise folks. Now I just remove option with the TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc , as I did not have this file. Then the program keep running. Did you mean that this option is not necessary for getting the fiber tracking?
Happy new year!
Rujing
by
charujing123
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AFNI Message Board
Hi Glen
Thanks.
As you said, they are not in common system. If we are interested in the group analyses, any suggestions?
rujing
by
charujing123
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AFNI Message Board
Hi Peter
Thanks
Did you mean that, for the subcortical, we can only perform the volume-based analyses? And we can use the segmentation (eg. freesurfer) with 3dSurf2Vol to get the subcortical (volume based) analyses.
Is that right? If so, how to get group analyses, as they are not in common space.
rujing
by
charujing123
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AFNI Message Board
Hi
1,if the phase was the LR and RL, should I choose the slice?
2,The registration settings file /home/zhangxiaochu/zharj/DIFF_PREP_WORK/TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc does not exist.. Exiting
this is the script:
===
DIFFPREP \
--dwi $odir/LR.nii
by
charujing123
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AFNI Message Board
Hi
In server without GUI, so it echos errors like title. To make sure that the pipeline going on, how to rescript this command:
# I/O path, same as before
set path_P_ss = data_proc/SUBJ_001
fat_proc_select_vols \
-in_dwi $path_P_ss/dwi_00/ap.nii.gz \
-in_img $path_P_ss/dwi_00/ap_sepscl.sag.png \
-prefix $path_P_ss/dwi_01/dwi_sel_ap
fat_
by
charujing123
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AFNI Message Board
Hi,
If within each session, oblique axial acquisitions alternated between phase encoding in a right-to-left (RL) direction in
one run and phase encoding in a left-to-right (LR) direction in the other run; how to use the LR and RL data into the afni_proc.py?
Thanks.
rujing
by
charujing123
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AFNI Message Board
Hi
if I am interested in the striatum (subcortical), can i still perform surfaced based analysis?
Thanks.
rujing
by
charujing123
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AFNI Message Board
Hi rick
The full path is still not working, but using current directory is OK.
So the problem is solved.
Thanks for your help.
rujing
by
charujing123
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AFNI Message Board
Hi
I am trying to run
====
set path_P_ss = data_proc/SUBJ_001
fat_proc_select_vols \
-in_dwi $path_P_ss/dwi_00/ap.nii.gz \
-in_img $path_P_ss/dwi_00/ap_sepscl.sag.png \
-prefix $path_P_ss/dwi_01/dwi_sel_ap
====
However, i only have nii for dti, not dcm files. So i did not run dcm to nii, then no png for this command. Is there any command
by
charujing123
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AFNI Message Board
Page 1 of 4
Pages: 1234