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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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Hello,
I am thinking of upgrading my machine and I am wondering if anyone has tried this setup yet.
Cheers,
Gerome
by
GMan
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AFNI Message Board
Hey All,
I am running MAC OSX 10.15.4 and cannot run afni
Here is the output from afni_system_check.py
Geromes-MacBook-Pro:~ gerome$ afni_system_check.py -check_all
-bash: afni_system_check.py: command not found
Here is the output from where I think the problem is:
Geromes-MacBook-Pro:~ gerome$ cd
Geromes-MacBook-Pro:~ gerome$ curl -O
% Total % Received % Xferd Average
by
GMan
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AFNI Message Board
Here is the code (looping through all conditions analyzed)
cd results/
foreach file_s (*.txt)
set cond = "`echo "$file_s" | cut -f 1 -d '.'`"
mkdir ${cond}/
RBA -prefix ${cond}/${cond}_Result -Subj Subj -ROI ROI -Y Y -chains 4 -iterations 1000 -model 1 -EOI 'Intercept' \
-PDP 7 6 -dataTable $file_s
unset cond
end
I will message you
by
GMan
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AFNI Message Board
Hello,
I have recently run an RBA analysis on regions of interest and would like to create a boxplot similar to Chen et al., 2019 to report the effects for each region. I am completely new to R so any guidance is appreciated.
Cheers,
Gerome
by
GMan
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AFNI Message Board
Hello,
I have a 5 condition repeated-measures design. I am interested in the effect of condition on activation levels in 21 regions of interests (as determined by previous studies). The contrasts of interest between relevant conditions were computed at the first level.
Is it possible to use BayesianGroupANA.py to determine the likelihood that the ROIs were activated in response to each co
by
GMan
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AFNI Message Board
Hello AFNIers
Is it possible to extract the average timeseries of all voxels in an ROI?
Cheers,
Gerome
by
GMan
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AFNI Message Board
Hi Daniel,
Thanks for your help, I will try it.
I am trying to share some statistical fmri results with a team of radiologists who don't use AFNI. A few of them want to see all 176 slices.
I was thinking of just putting it in powerpoint as animations and they can scroll through them.
Cheers,
Gerome
by
GMan
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AFNI Message Board
Hello AFNI community,
Is it possible to save every slice in the AFNI viewer as a separate image?
Cheers,
Gerome
by
GMan
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AFNI Message Board
Hello,
In one of my runs, the participant missed the start of the first block (1 out of 10) in my 24 s block design in one run. They did initiate a response 17 seconds into the block but the response only lasted 7 seconds (as opposed to 24). The participant did well in all other blocks in all other runs.
Would it be best just not to include this block in the analysis (by taking out the c
by
GMan
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AFNI Message Board
This is what it outputted (although I asked about two tasks (I did it to simplify my question) my experiment actually contains 9 tasks with 9 different conditions )
* ISI error: stimuli overlap at run 1, time 46.0,overlap 30.0
** ISI error: stimuli overlap at run 1, time 104.0,overlap 33.0
** ISI error: stimuli overlap at run 1, time 167.0,overlap 36.0
** ISI error: stimuli overlap at run
by
GMan
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AFNI Message Board
> Are you saying that you didn't have collinearity when analyzing each run separately but you did when the two runs were concatenated? If so, something was not properly specified in the latter situation.
Yes this was indeed the case. In my afni_proc for the concatenated multiple task runs this is what I used to define the model:
regress_stim_times ${subj}/afni_folder/B*afni_task*.tx
by
GMan
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AFNI Message Board
Thank you both for your response I was getting the following warnings when concatenating the runs- where the task in run1 is "step" and the task in run2 is "stand".
++ Wrote matrix values to file X.nocensor.xmat.1D
++ ----- Signal+Baseline matrix condition (1278x155): 3.58672 ++ VERY GOOD ++
[7m*+ WARNING:[0m !! in Signal+Baseline matrix:
* Largest singular value=
by
GMan
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AFNI Message Board
Thanks for the response.
Would concatenating the two runs of data be correct if the baseline conditions in each run were different?
I actually tried running a model wherein the tasks are concatenated- 3dDeconvolve in this case outputs colinearity warnings (becuase run 1 is highly correlated with the regressor for task 1 and run2 is highly correlated with the regressor for task2). I am un
by
GMan
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AFNI Message Board
Hello,
I am wondering how to implement a paired t-test in 3dMema.
I have a dataset wherein participants are exposed to the same stimulus during two different tasks (taskA and taskB). 10 Participants perform taskA in run 1 and taskB in run 2. During each run they are exposed to six 30 second blocks of the stimulus.
For the first level analysis I have modeled the runs separately (as the
by
GMan
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AFNI Message Board
Hello,
I have been given some data and within the afni analysis folder there are this file outlining the onset and duration of a stimulus presented in the first 6 runs (there are 9 runs in total):
45:30 103:33 166:36 238:39 309:33 382:39
45:30 103:33 166:36 238:39 309:33 382:39
38:30 96:33 159:36 231:39 302:33 375:39
45:30 103:33 166:36 238:39 309:33 382:39
45:30 103:33 166:36 238:3
by
GMan
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AFNI Message Board
I have a dataset where participants performed: two tasks under two conditions
Let's say the design looks like this:
TaskA - condition1(TAc1)
TaskA - condition2(TAc2)
TaskB- condition1 (TAc1)
TaskB- condition2 (TBc2)
Based on the literature a am interested in looking at the differences in activation between tasks and conditions in 30 regions of interest. I also would like to use a
by
GMan
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AFNI Message Board
Hello,
I have a dataset where the same protocol was collected on participants in two different scanners. The final resolution of the images from the first scanner was 1.5mm x 1.5 mm x 1.5 mm (after preprocessing- alignment, motion correction registration). The final resolution of the images from the second scanner was 2.5 mm x 2.5mm x 2.5 mm (after preprocessing).
What would I need to do
by
GMan
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AFNI Message Board
Hello,
I constructed a mask containing 41 spherical ROIs . If in my analysis I am only interested in activation within these ROIs - how do I determine the cluster threshold for interpreting the results of 3dttest++ ?
I tried running 3dClustsim on the custom mask I created and got the following results: these numbers seem low to me (but I am new to fmri analysis).
CLUSTER SIZE THRESHO
by
GMan
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AFNI Message Board
Hello,
I have a data set with 6 runs. In each run the participant are doing a task (resting*2, simulated standing *2, and simulated walking *2) . Participants complete these tasks either in the presence or absence of simulation (30 seconds of no stimulation followed by 30 seconds of stimulation in alternate blocks for the duration of each run). I have been asked to determine the difference i
by
GMan
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AFNI Message Board
I figured out there was an error in my code - I was missing at "glt label 10" however- I am new to FMRI and could still use some guidance on analyzing these data.
Cheers,
Gerome
by
GMan
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AFNI Message Board
INFO:
- AFNI ver: AFNI_19.1.00
Hello AFNI team,
I am currently struggling with my approach to analyzing individual participants in my fmri dataset: The data for each participant consists of 6 runs of 417 seconds. In each run the participant are instructed to do a different task classified as:
1. rest15, ( the numbers in the task names have nothing to do with durations)
2. stand15,
by
GMan
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AFNI Message Board