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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 AFNI guys (probably Gang):
I used 3dMVM to run an analysis on my data which is from a 3x2 within-subject design; i have 3 stimuli and 2 (qualitatively different) runs and 3 covariates - Sex, STAI-T, STAI-S. Everything ran fine and I used the code attached.
3dMVM -prefix /Volumes/SEQUEL_DISS/PRO_AFNI/OUTPUT/derivatives/STATS/whole_brain/MVM_TvsC_covars.nii.gz -jobs 4 \
-bsVars "sex
by
lhopkins
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AFNI Message Board
Hi Gang:
I am writing a 3dMVM script for a scan where a participant saw 6 stimuli. Each stimulus was different but there were 3 categories of stimuli (i.e. CSp, CSm, CSt) and 2 exemplars of each. Thus the stimuli were CSm1, CSm2, CSp1, CSp2, CSt1, CSt2.
My Question: Some of the contrasts I am interested are, for example, ALL of the CSms vs. ALL of the CSps (similar to the emotional vs. neu
by
lhopkins
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AFNI Message Board
Thanks Gang!
Sorry my second question wasn't clear but you basically interpreted it correctly. That's what I thought as well (it not being feasible at the event related level) but it's nice to have it confirmed.
Two final questions: I've used PROC_PY to generate my preprocessing scripts for the first analysis run-through. For the final analysis I am using 3dREMLfit to get
by
lhopkins
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AFNI Message Board
Hey everyone:
Sorry for the beginner question. I want to look at the response of a particular ROI to stimuli on a trial-by-trial basis. After performing a more 'traditional' ROI analysis on the beta weights of (e.g.) the amygdala I found no difference in the amygdala's response to different stimuli but I believe this is in large part because the amygdala habituates quickly. So b
by
lhopkins
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AFNI Message Board
Hey all:
I have 2 independent questions that have arisen from the same problem.
Basically I'm trying to code some TCSH scripts with cool tricks that make the scripts more "all-purpose" and have gotten stuck in a few places.
1) Firstly I was trying to make anatomical masks with atlases for which certain anatomical areas are made of multiple parts from the atlas (e.g. NOT usi
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lhopkins
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AFNI Message Board
Hey Rick:
Hate to bother you with this again. So running
brew install matplotlib
doesn't actually work anymore. I guess it migrated? Anyway, to get that specific code to work now you'd do:
brew tap brewsci/science
brew info brewsci/science/matplotlib --json=v1
brew install brewsci/bio/matplotlib
The reason I'm posting is that, while this code will run, it installs matp
by
lhopkins
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AFNI Message Board
Hey guys:
I am having problems running the review driver script that is outputted from the following command:
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
After some previous output the error is as follows:
AFNI QUITTs!
\n+* Removing temporary image directory 'QC_sub-S14V1A/media/__tmp_chauf_zB5fIsj7aot'.\n
[1] Done
by
lhopkins
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AFNI Message Board
Hi Rick:
Thanks for your response! The identity solution seems completely reasonable, thank you for suggesting it.
I was having issues aligning my T1 to my EPI. Daniel suggested that the skullstrip was, ironically, doing TOO GOOD of a job and removing some CSF that could have been used to better align my EPI so the solution was a dilated version of skullstrip. However, I have performed both
by
lhopkins
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AFNI Message Board
Hi guys:
Please forgive this very specific question. I just attended an AFNI Bootcamp (best 5 days of my life) where as part of the handouts you guys provided us with some "c" and "p" scripts in an "AFNI_pamenc" folder.
I was enthralled by how streamlined these scripts made things so have edited them for my own purposes. I have had some registration issues, tho
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lhopkins
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AFNI Message Board
Hey Rick:
Thank you for that. This solved the problem. Specifically thanks for the explicit instructions as I did have to change the dot file and "reinstall" pyqt4 via conda.
I appreciate it very much - I never would have figured this out on my own.
Thanks for your time.
Lauren
by
lhopkins
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AFNI Message Board
Hey guys:
I used to be able to run Uber-subject.py without issue but today when I went to run it it literally just gives me "Segmentation Fault."
Running it with sudo is slightly more helpful and gives me
`**** failed to import PyQt4.QtGui ****
PyQt4 must be installed to run the uber_subject.py GUI
--> see the output of: uber_subject.py -help_install`
I'm
by
lhopkins
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AFNI Message Board
Hi everyone. This one is probably for Gang,
I have 2 quick questions about 3dLME syntax.
Currently I have 2 within-subjects fixed variables - cs (csm, csp, cst) and scan (scan1, scan2) - and I'd like to investigate the difference between each cs within the same scan and between the same cs between the two scans. So I'd like t-test between csm & csp, csm & cst, and csp &
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lhopkins
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AFNI Message Board
Hi Daniel:
Am I misunderstanding that the MNIA atlases are not actually in MNI space but in some variant thereof?
I had assumed they were capable of being used with any analyses in MNI space because there are only templates included here and this link here seems to allow downloads of just the Eickhoff and Zilles files as you stated above.
If so, are the other atlases anywhere specific? I
by
lhopkins
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AFNI Message Board
I just did this for the amygdala in MNI space so this'll probably work for you.
whereami -mask_atlas_region CA_ML_18_MNIA::Putamen
Remember you're not using the TT atlas you're using the MNI atlas to get your ROI so you have to indicate that after the -mask_atlas_region flag.
A note though: This gives you the bilateral putamen because of the :: part of the code. If you wan
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lhopkins
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AFNI Message Board
This helps a lot, Gang. Thank you very much for your help.
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lhopkins
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AFNI Message Board
Hey guys,
I'm mostly used to using AFNI group level analysis tools I started out with like the 3dANOVAs but realize the new abundance of tools available for mixed modeling options and am wondering if one of those would better fit my situation than what I have previously used.
Currently I have a completely within-subjects design with 2 within-subjects variables. Variable 1 has 3 levels
by
lhopkins
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AFNI Message Board
Hey Dan:
Just wanted to thank you for this. This is truly the clearest and most concise description of any of this data that I've gotten so far. I was able to get an appropriate RetroTS output from your guidance although I'm not exactly sure how useful the regressors will be given the issues with the data you specified.
I mostly just wanted to be able to make informed choices with
by
lhopkins
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AFNI Message Board
Hey guys:
To follow up on this - I read in a post on another forum that generally the raw physiological data should be used as input to a variety of software. If this is the case for RetroTS, my cardiac and respiratory data have different sampling rates (PPG: 10ms, RESP: 40ms). If I'm just inputting the raw data should I:
1) Downsample the PPG
2) Upsample the RESP
3) Run RetroRS separa
by
lhopkins
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AFNI Message Board
Forgive what will be a series of very beginner questions.
I have never processed physiological data from scratch before. We use a GE Healthcare Discovery MR750 3T MR System and obtain PPG and RESP data.
My first issue is I have not been able to find online WHAT exactly the y-axis is when the data is obtained. I understand the PPG, "Pulse monitoring uses a photopulse sensor to detect blood
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lhopkins
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AFNI Message Board
Great, thank you both for your replies. I've seen weird techniques in other softwares and it's nice to be able to use a pipeline I'm familiar with and not employ corrections when I'm not sure how they work.
Appreciate your time. Thank you.
by
lhopkins
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AFNI Message Board
Hey everyone:
I'm going to be running an experiment consisting of 3 runs of fear conditioning acquisition data (8 minutes each) which was originally part of a single 24-minute run. We made this change to account for subject comfort and to hopefully decrease the motion that would have been associated with being in the scanner for so long in the 24-minute case. I have two questions I wanted
by
lhopkins
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AFNI Message Board
Hey guys, I have a theoretical question.
I'm running 3dDeconvolve on simulated data to check out an experimental design. I've read the 3dDeconvolve manual but it's dated 2001 when stim_file was the norm. I had emailed Doug Ward some questions that he was awesome enough to answer and he recommended for my simulations, to use binary stimulus timing files and the stim_file option i
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lhopkins
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AFNI Message Board
Hey guys:
I'm using the 3dDeconvolve -nodata option to test some experimental designs. Quick questions.
1) Each stimulus is 12s so I originally made a binary file as input as per the manual Doug Ward wrote in 2002 where I treat each stimulus as a sequence of 6 1s in a row (2s TRs) so each stim_file essentially looked like this - 0 0 0 0 1 1 1 1 1 1 0 0 0 - and there were 3 of those. Howe
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lhopkins
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AFNI Message Board
Hi Gurus:
I have a couple of questions, two theoretical and one technical. I think the theoretical ones will make more sense if I ask the technical question first.
Technical question: I am going to run an experiment where I present a stimulus (CS) paired with a shock which occurs at different times during the stimulus (but the shock occurs on every trial). The CS itself will always be prese
by
lhopkins
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AFNI Message Board
Hi Rick, thanks for your response.
Quoterick_reynolds
Are you clustering in orig space? If so, why? Also, why go
to 1x1x1 at the end, and not something closer to the original
resolution?
Te long story short of it is that we did all of our data analysis and write up on data using techniques from before that Ecklund paper came out - basically the whole processing pipeline and subsequent wr
by
lhopkins
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AFNI Message Board
Hi Gurus:
I've gone though the entire process of using 3dFWHMx and 3dClustSim to get cluster thresholding values.
I understand that it is more accurate to run 3dClustSim with a mask that is the same dimensions as what you got off the scanner so that's what I did. Basically I ran 3dFWHMx on the 4x1.8x1.8 .errts files and got the acf values from that and then used a 4x1.8x1.8 mask fi
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lhopkins
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AFNI Message Board
This is perfect, Rick!
Thanks so much for taking the time.
Lauren
by
lhopkins
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AFNI Message Board
Hey Gurus:
I know you can do this with BASH commands but given this is part of the new way to do cluster correction I figured this might help others so I decided to post it.
I am in the process of doing the new cluster correction procedure.
I have run FWHMx on my subjects' residuals and gotten out the relevant acf a,b,c parameters.
I have taken these parameters and put them each into
by
lhopkins
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AFNI Message Board
Hi Gurus:
I recently changed my Mac OS to Sierra and for simplicity just uninstalled AFNI with the intention of reinstalling it because a lot of stuff got messed up in the OS change over. I'm stepping through the 'essential system setup' and am on Step 2. For the most part things are going ok but I'm getting a decent amount of ERRORS that look like the following:
** ERRO
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lhopkins
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AFNI Message Board
Hi Guys:
So we're in the process of making some anatomy-based ROIs from FreeSurfer segmentation files. We've run our EPI and anatomy data through most of a uber_subject preprocessing pipeline and will ultimately be wanting to do all of our analyses in a standardized space. I had figured that we could just take the aparc_aseg.mgz file that comes out of FreeSurfer and use the cat_matve
by
lhopkins
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AFNI Message Board
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