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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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Results 1 - 30 of 31
Hi Paul,
Thanks for your quick reply. When specifying -olay_alpha Yes -olay_boxed Yes, is there a way to then also account for the cluster extend threshold of k =10 that was suggested in the preprint? So far, I could get Example 5 to work with a lenient p=0.05 showing highlighted data, but not accounting for the suggested cluster size k=10. Likewise, I can get Example 6 to work where 3dCluster
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s.meliss
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AFNI Message Board
This is a really interesting proposal on result reporting, thank you very much for this.
Is there some example code on how to produce Figure 1F (Response map: highlighted) using the proposed lenient thresholding of p = 0.05 and k = 10?
Many thanks,
Stef
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s.meliss
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AFNI Message Board
* Job title: Junior Research Group Leader (100%, E 14 TV-L) or Postdoctoral Research Fellow (100%, E 13 TV-L) on Cognitive and Affective Neuroscience
* Location: Hector Research Institute of Education Sciences and Psychology
* (Initial) Deadline: September 30, 2021
* Job description
We are seeking postdoctoral researchers on cognitive and affective neuroscience (broadly defined, but we
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s.meliss
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AFNI Message Board
Hi Gang,
In our 3dISC analyses, we are interested in the effects of a between-subject variable (our experimental manipulation), a behavioural covariate (ratings obtained during naturalistic viewing) as well as their interaction. Specifying an initial p-value of 0.001 cluster-extend thresholded (k=32) to achieve alpha = 0.05, I find effects of group and the covariate, but no interaction. Howeve
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s.meliss
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AFNI Message Board
Hi Gang,
Thanks for your reply.
Could you please clarify what you mean when asking how the results look to me? I have read the paper you linked and liked the suggestion of reporting a highlighted response map with little to moderate thresholding.
In total, I have anatomically defined 4 ROIs, all subcortical. Hence, I was wondering whether there is either any "small volume correction
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s.meliss
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AFNI Message Board
Hi AFNI team (or better: hi Gang),
I would like perform ISC analysis on whole-brain level as well as for a list of a priori defined ROIs. In addition to synchronicity overall, I am also interested in the effects of group and other covariates as well as their interaction. Thus far, I have used 3dISC for whole brain analysis specifying a grey matter mask, thresholded the results using p = 0.001
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s.meliss
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AFNI Message Board
Dear Bob,
Thank you for your reply and for pointing out the issue of averaging correlations related to non-linear transformations.
Is there any way to actually derive the "mean of correlation" to threshold the maps at r=0.3?
From what I understand after discussing this with my supervisor, there are (at least) these three options:
Use 0th sub brick showing mean of arctanh(cor
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s.meliss
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AFNI Message Board
Dear AFNI experts,
I hope everyone is well! I have a (hopefully quick) question about the output of 3dGroupInCorr.
I ran:
cd "$deriv_dir" # change directory to where pre-processed files are
# define prefix
out_GroupInCorr=FC_task-"$task"_wholebrain_pearson
# set up FC
3dSetupGroupInCorr -mask $code_dir/$epi_mask_rest -prefix "$FC_dir"/$out_GroupInC
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s.meliss
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AFNI Message Board
Hey Paul,
Thank you for your reply. I successfully managed to install from the local copy without further problems.
With respect to the R installation, should I also save e.g. the @add_rcran_ubuntu_18.04.tgz in the same directory to install the corresponding R dependencies for the AFNI version I installed now, or are there no variations over time?
Also, thank you for your suggestion, th
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s.meliss
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AFNI Message Board
Dear AFNI experts,
I have some questions regarding the installations of AFNI on virtual machines (linux based system). Our IT structure requires us to access and analyse fMRI data using linux-based virtual machines (VM), but the VMs expire after one month. Every time when I launch a new VM, I need to install AFNI from scratch. For that I usually follow the instructions here. The problem is eve
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s.meliss
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AFNI Message Board
Hey Paul, hey Rick,
Happy New Year!
Thanks for your response and sorry for taking some time to reply, I needed to think about what you both said.
I think it might be helpful to give you a bit more background on the data: we acquired a 10 min (TR = 2, 300 volumes) resting-state scan before subjects participated in an incidental learning paradigm where we displayed short movie clips and
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s.meliss
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AFNI Message Board
Hey Paul,
Thank you very much for this detailed answer, this is very informative and helpful.
I was not aware that "-regress_polort" is included by default - I am learning something about my friend afni_proc.py all the time One quick follow up question here: if I don't specify the DEGREE manually, it seems as if it is computed based on the length of the first run rather than
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s.meliss
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AFNI Message Board
Dear AFNI Gurus,
I hope you are enjoying this special time of the year even though it is a very different year.
I have a question regarding the pre-processing of resting-state data, especially with respect to bandpassing.
This resting-state-note states that the data should be bandpassed if physio recordings are not available. Unfortunately, we did not collect any physio recordings, hence
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s.meliss
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AFNI Message Board
Hey Paul,
To further follow up on the second part of your message: I again checked the output of the whole sample (50 subjects) and the initial alignment (init_qc_00_overlap_usrc_obase.jpg) after running @Align_centers was actually comparably good/bad across all of them - probably as suggested by you due to considerably large neck/cheek areas. Whilst this not-so-great initial alignment was ove
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s.meliss
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AFNI Message Board
Thank you for your reply, Paul, this is really appreciated. I am happy to upload the data if you provide me with instructions. I had added the SSopt-push_to_edge based on the 3dSkullStrip help for general clippings.
Best wishes,
Stef
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s.meliss
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AFNI Message Board
Dear AFNI experts,
I am trying to implement @SSwarper into my pre-processing and whilst the defaults (@SSwarper -input ${T1 file} -subid ${subject} -odir ${out_dir} -base ${template}) worked well for most subjects, some subjects had clippings in axial inferior slices. To combat this, I have updated AFNI (now running Precompiled binary linux_ubuntu_16_64: Nov 12 2020 (Version AFNI_20.3.02 '
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s.meliss
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AFNI Message Board
Dear AFNI experts,
I have a quick question regarding the MNI template (MNI152_2009_template_SSW.nii.gz) used in @SSWarper. Is it correct that this is the same as ICBM 152 2009c Nonlinear Asymmetric template?
Many thanks in advance,
Stef
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s.meliss
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AFNI Message Board
Hi Rick, hi Gang,
Thanks for your replies.
The participants did not leave the scanner between the two resting state runs, but there was a 45 minute task (including breaks) in between, so it might be that their head position was different between the runs.
I am planning to compute the connectivity (i.e. correlation) between two ROIs separately within run 1 and run 2 and then look at the
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s.meliss
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AFNI Message Board
Dear AFNI experts,
To follow up on this topic: given that all my resting state scans (pre and post task) have a duration of 600s (TR = 2s, hence 300 volumes) and given that the final .errts file has 600 volumes, would it be possible to simply split this file to create separate files for pre and post learning rest by selecting the first and second 300 sub-bricks respectively and save them? can
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s.meliss
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AFNI Message Board
Dear AFNI experts,
we collected resting state data from our participants before and after they performed a task (including between subject experimental manipulation). Each of these resting state runs lasts 10 minutes. We are interested in changes in resting state functional connectivity between MTL and midbrain and whether there are group differences in this and whether it relates to performan
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s.meliss
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AFNI Message Board
Dear AFNI experts,
I am new to AFNI and am trying to work out how to do the clustering on group level correctly.
From the handouts related to this topic I learned that afni_proc.py automatically estimates the smoothness of my data. In the $subj.results folder, there is a sub folder "files_ACF" containing an out.3dFWHMx.ACF.errts.r0*.1D file for each of my three runs. All three fil
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s.meliss
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AFNI Message Board
Hi Paul,
Thank you very much for your reply.
As indicated here (https://afni.nimh.nih.gov/afni/community/board/read.php?1,161034,161745#msg-161745) when doing what you've suggested I got an incredibly high number of motion censored volumes - even though the motion is not apparent in the original EPI files for each run which was very surprising for me. Hence, I tried to disentangle the
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s.meliss
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AFNI Message Board
Dear Paul,
I am sorry for bothering you again. I have pre-processed my data, but wanted to make sure that what I did makes sense. Please see below for how I specified the afni_proc.py -- I modified the pre-processing a bit compared to what was suggested in the NI paper: I am pre-processing the data separately for each run whilst regressing out the polynomial degrees (up the third order given
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s.meliss
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AFNI Message Board
Hi Paul,
Thank you for your reply. I tried to explore where in my pre-processing the high degree of censoring occurs. From how I understood your reply from April 12th, I firstly detrended each run, then took each each clip, demeaned it, unshuffled it and combined it into one nifti file which I then used as input for the pre-processing following the same code as used in Chen et al (2016, NI) wi
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s.meliss
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AFNI Message Board
Dear Paul,
I came across some problems in the pre-processing related to a very high number of volumes getting censored due to motion. I acquire my data in three runs and participants have breaks in between them, so it could be that they move their heads in the breaks but not during the EPI acquisition itself. But given that the current pre-processing pipeline firstly reassembles/unshuffles the
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s.meliss
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AFNI Message Board
Hi Paul,
Thank you very much for your thorough reply. To sum it up: you would advice to detrend first, then to cut the time series corresponding to each video clip, demean, reorder and concatenate them and run the preprocessing on the resulting data series. For the preprocessing, the code from the NI paper can be used, but -regress_polort 0 should be added. The resulting output (errts* file) c
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s.meliss
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AFNI Message Board
Dear AFNI experts,
In my study, participants view short video clips (average duration 32 seconds, 36 in total) pseudo randomised across three runs (i.e. 12 video clips per run) and are asked to rate the clips they have seen. I am currently planning the preprocessing (based on ) and have a couple of questions I would highly appreciate your thoughts on.
Firstly, if I am interested in subcorti
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s.meliss
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AFNI Message Board
Dear AFNI experts,
During my experiment, participants watch 36 short movie clips (average duration 32 seconds) over three runs (i.e. 12 clips in each run) and are asked to give ratings after each clip. The order of movie clips is pseudo-randomised across participants and runs.
I am planning to follow the preprocessing as described by Chen et al. (2016): and have some questions about it:
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s.meliss
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AFNI Message Board
Hi Rick,
When I type afni, that is the output:
Last login: Tue Aug 7 19:19:02 on ttys001
webvpn-19:~ stefaniemeliss$ afni
Precompiled binary macos_10.12_local: Jul 31 2018 (Version AFNI_18.2.06)
Thanks go to DA Jacobson for inspiration
Initializing: X11
++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when
+ opening windows, or you cannot type text into AFNI popu
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s.meliss
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AFNI Message Board
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