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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
According to the documentation you get interactions between the factors listed in -bsVars and -wsVars. That explains why I got the the interaction between AUQ1 and Stim. But to get the interaction between the two -bsVars" Treatment and AUQ1" the documentation sais that i should use colon : and not asterisk *. Asterisk meant A+B+A:B. So should it be:
1). (original version)
3d
by
Robin
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AFNI Message Board
Thank you Gang!
QuoteGang
> Is the script + table correct for this experiment?
The following 3 lines
-gltCode 1 'Treatment: 1*real -1*sham' \
-gltCode 2 'Stim: 1*alc -1*non_alc' \
-gltCode 3 'Treatment: 1*real -1*sham Stim: 1*alc -1*non_alc' \
should be changed to (add a space before each colon)
-gltCode 1 'Treatment : 1*real -1*sham' \
by
Robin
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AFNI Message Board
Hi AFNI experts.
I ran a pre-processing pipeline that gives, for task data, stats files for data processed both with and without ANATICOR (-regress_anaticor_fast).
From my understanding ANATICOR uses WM masks to estimate noise coming from e.g. the scanner and coils. It also should reduce white matter clusters (right?).
When running a group analysis using 3dMVM on 36 subjects and looking
by
Robin
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AFNI Message Board
Hi! I have some questions regarding 3dMVM and if it's set up correctly...
We have data from patients who get treatment (REAL vs SHAM) and they watch stimuli (pictures of ALOHOL vs Non-ALCOHOL). In previous analysis I have used 3dMVM since the groups are uneven. Typically like this:
3dMVM -prefix no_covariates -dataTable @table.txt -jobs 10 \
-mask mask+tlrc \
-bsVars Treatment \
by
Robin
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AFNI Message Board
Replying to my own post.
Now the results look identical. -nlast seem to refer to the index so -nlast 300 means sub-brik 0-300 which is line 1-301 in the censor file.
If you can confirm that this is correct I guess you can remove this post if no one else would find it helpful.
Thanks!
by
Robin
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AFNI Message Board
Hello AFNI masters,
We have preformed a "standard" afni_proc.py pre-processing procedure and now want to deep dive a little by focusing only on the first 5 min out of a 7 min scan since we have some biometric data (blood samples) that only span over the first 5 minutes. We simply feed the pre-processed (wapred pb04.subjX.blur+tlrc) data into a new 3dDeconvolve command with our new sp
by
Robin
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AFNI Message Board
Hi and thanks!
It is quite strange. Depending on the order you do things the error some times does not occur. But you get the "connection to 3dGroupInCorr is broken" a 100 % of the times if you do:
afni -niml &
3dGroupInCorr -setA file.grpincorr.niml
Overlay: file.grpincorr
Setup GICor (set seed radious) Set + Quit
Change OLay and Thr to Z-scores
Clusterize (20) Set+ Qu
by
Robin
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AFNI Message Board
Hi gurus...
We have been been having some issues when dynamically working with 3dGroupInCorr (when being logged in remotely on a server with afni installed). The user computer is a Windows Computer and the same issue occurs when connecting via either MobaXterm or Putty.
Quoteproblem description
I am doing an exploratory functional connectivity analysis. So I combined the resting state files
by
Robin
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AFNI Message Board
That's good! It felt kind of counter intuitive but I get it now!
Thanks Rick!
by
Robin
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AFNI Message Board
Thanks, that can explain the smoothed look of the time series in the middle slices.
I did:
$ 3dinfo -orient pb01.rest1_14.r01.despike+orig.
RPI
This indicates that the Z-coordinate (or k) goes from low/neg to high/pos when travelling up the stack. Which is what i see in the viewer as well. Attaching print screen of the despike time series (top) and the tshift time series (bottom) of the mo
by
Robin
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AFNI Message Board
Thanks, I'll check tomorrow. But I am right in that the shift should be "to the left" if all was good, right?
by
Robin
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AFNI Message Board
Hi again, a follow up question!
We have linearly collected ascending slices (feet to head) and we are confused about using -z or +z. From previous responses it sounded like -z was correct but +z (from feet to head) is how the data is collected (assuming positive z-axis from feet to head).
When using -tpattern seq-z (and the default -tzero set to 0) we expect the top slice to stay the same
by
Robin
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AFNI Message Board
Thanks Rick!
But this is true even if the volume is from another run?
Then I can keep my current set-up which is first preforming a localizer task where the EPIs are volreged to the min outlier and then the anatomy is aligned to that epi volume. Then you draw a ROI of your choice on the anatomical . Then during the real time feedback run the EPIs are aligned to the minimum outlier epi of th
by
Robin
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AFNI Message Board
Hi!
I just wonder if it matters what volume you align to when it comes to motion regressors. Assume we don't do any warping, just the align block and for some reason (in this time real time fMRI) want to align the EPI volumes to an EPI volume from a previous run (localizer or seed mask from a pervious run). When preforming the regression of the current run with the motion regressors, will
by
Robin
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AFNI Message Board
Well, the values are not missing.Blood samples were simply not matched with one blood sample per condition but one sample per person touching them (just three samples over time for each toucher).
I guess you could collapse the arm/palm regressors to just beeing touched and compare beeing touced by P_1 and P_2 and using the two BLOOD samples as covariates BLOOD_P1 and BLOOD_P2?
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Robin
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AFNI Message Board
Thanks!
I'm not sure exactly what they want to do. They have these ratings and want to incorporate these in some way. Since the ratings differ they expect to see some of the brain to correlate with rating. So comparing b1 makes sense but running a group analysis with 3dttest++ comparing the b1 maps for e.g. arm and palm gives no significant voxels, even though the rating means are differe
by
Robin
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AFNI Message Board
Hi!
QuoteGang
One thing needs clarification: Is the duration for each trial correlated (or confounded) with the pleasantness rating? If so, modulation analysis would be a little bit shaky.
Each Condition (A-D) has 3 onsets per run. They run 2 runs so each condition has a total of 6 onsets. Each onset has a fixed duration of 10 s (no correlated to pleasentness).
QuoteGang
They would not
by
Robin
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AFNI Message Board
Hi Gang!
Sorry for a late reply, I have been away.
QuoteGang
Let me try to understand the situation. You have two conditions, A and B, each of which has 3 trials. Each trial lasts for 10 seconds. In addition, you have behavioral data (pleasantness) that are associated with each trial. Is this accurate?
First of all, the number of trials per condition seems too few to achieve a robust est
by
Robin
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AFNI Message Board
Thanks Rick!
0) The means are not really that different. I just gave an example.
QuoteRick
Note that the mean applied to each modulator actually affects
the beta of the mean response, rather than the beta of the
modulated on.
1) Can you re-center across Conditions in a "normal" un-modulated analysis approach (e.g. stim times)?
2) We previously established that the mean re
by
Robin
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AFNI Message Board
Thanks Rick!
I'm not 100 % sure how to do this practically though. If we have:
Subject1:
CondA: 10*2 30*4 50*1
CondB: 20*8 40*7 60*9
Subject12
CondA: 10*1 30*2 50*2
CondB: 20*9 40*8 60*9
First off, we want to find the regions (where bold is modulated by / following the ratings) where the modulated CondA and CondB are different. So to the very least we want to center the modulat
by
Robin
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AFNI Message Board
Hi!
We have an experiment where the subjects rate two different stimuli. Let's say condition A and B where each have 3 onsets of duration 10 and each onset has a rating of pleasentness connected to it.
What we have done is first to run a non-modulated GLM where we just have the onsets and durations. The gives a X.stim.no.censor file where A and B each have 3 spikes/onsets and they have
by
Robin
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AFNI Message Board
Hi!
I convert our DICOMS to .nii via dcm2niix and when running 3dinfo -slice_timing ../../data/sub01/rest1.nii I got worried:
3dinfo -slice_timing ../../data/sub01/rest1.nii
** AFNI converts NIFTI_datatype=4 (INT16) in file ../../data/sub01_TF/rest1.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to se
by
Robin
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AFNI Message Board
Thanks! I guess it must be OK since the standard output of afni_proc.py for resting state data is to create an X.mat with all drift regressors (3dD with -polort A) and then to run 3dTproject with that matrix but also with -polort 0.
Thanks :)
by
Robin
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AFNI Message Board
Thanks Rick!
This made me think of a follow up question related to the relationship between 3dDeconvolve and 3dTproject:
When running a typical resting state pre-processing with Anaticor the X-matrix is generated by 3dD usually with a polort of 2 or 3. I.e. the X.mat contains these drift regressors.
But when running the 3dTproject command with this X.mat (and anaticor regressors) the pol
by
Robin
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AFNI Message Board
Sorry for beeing unclear!
Ok, so the newest version runs, when using anaticor, both 3dD and 3dREMLfit? That is what our version does, I get both the stats file and the stats.REML file.
So the question is if it is worth the extra time and the loss of DOF to run BP filtering. You have me pretty convinced, I'm not a huge fan of BP either. But we did see improvments a while back when we ra
by
Robin
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AFNI Message Board
Hi Rick!
QuoteRick
So you intend to apply exactly 1/3 of the degrees of
freedom to bandpassing? Note that a frequency of 0.37
would not cover the main components of heart rate or
breathing, for what little that is worth.
Hmm, that's true. In the afni_proc.py examples 0.01 and 0.1 is used. I know you don't reccomend BP overall but if we want to use it with a TR of 0.901 what limit
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Robin
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AFNI Message Board
Hi!
We have seen some improvements when including bandpass filtering on task data as well as resting state data. With a TR of 0.901 s we figured to basically use a low pass filter by setting the first argument to a very low number (0.001) and the second argument to 1 / (TR *3 ) = 0.37. I.e.:
-regress_bandpass 0.001 0.37
(for a TR of 2 this would be 0.001 0.17).
What I have realized is t
by
Robin
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AFNI Message Board
This was very helptful :). Thanks! And have a happy midsummer!
by
Robin
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AFNI Message Board
Thanks!
Just a final follow up: If 3dTproject can handle more complicated regressors (e.g. ANATICOR) AND it's faster than 3dDeconvolve, why is it not used instead of 3dD for e.g. a simple task analysis (no ANATICOR)? Can't it produce the stats file?
Best
Robin
by
Robin
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AFNI Message Board
Thanks Rick!
This makes so much sense! I guess what I have seen is that the generated procs look different between resting state and task based analysis since there usually are no regressors of interest in the resting state paradigm. Then afni_proc.py generated a command 3dTproject on the X.mat instead of running 3dDeconvolve (i.e. -x1D_stop in 3dDeconvolve and running 3dTproject after). Does
by
Robin
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AFNI Message Board