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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:
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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
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I am reviving this thread because 3dROIstats is behaving weirdly using my surface parcellation. I think I've found a solution, but also maybe a bug?
(In narrator voice) Previously on this thread:
I converted a Freesurfer annotation to .niml.dset using FS_read_annot, then I resample it to -ld 60 and ranked the node values so that 3dROIstats could handle the parcel labels.
I am no
by
dmoracze
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AFNI Message Board
Further update / solution, in case there are others trying to convert a Freesurfer annotation to SUMA surfaces.
The issue arose because Freesurfer's annotation values are so massive (almost all are greater than 32767). I used 3dRank to lower the annotation values to something more reasonable, which gave me the expected 3dROIstats output.
Thanks to Pete Molfese for the suggestion!
ED
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dmoracze
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AFNI Message Board
Update / consolidation on this issue:
I believe the issue is with how 3dROIstats is handling surface annotation datasets (or this surface annotation in particular).
I have checked the dataset created from FSread_annot, and everything looks to be in order. The regions are colorized as they should, and each node has a label that corresponds to freesurfer's "annotation value":
by
dmoracze
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AFNI Message Board
As an addendum:
I should be getting 200 regions per hemisphere, but instead 3dROIstats is giving me 39.
I have attached an image of the ROI file. It looks like 3dROIstats might be averaging over the colored regions, but, under the hood each of those regions are further subdivded.
by
dmoracze
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AFNI Message Board
Hello,
I am trying to convert a publicly-available surface parcellation to standard mesh in order to extract mean timeseries for connectivity analysis. My current method does not work as expected (explained below), but I'm also wondering if there is a more straight forward implementation.
I am using 3dROIstats to extract the timeseries, but the number of columns in the resulting files
by
dmoracze
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AFNI Message Board
They are within-subject factors.
Our event-related design is a 2x2 factorial. There is a factor of social partner (peer or computer) and type of reply to a questions (agree or away). So there are 4 conditions nested within two factors.
Currently I am taking your previously-suggested approach and extracting the 1st level beta values from the post-hoc contrasts peer-comp.agree and peer-comp.a
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dmoracze
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AFNI Message Board
Thanks for the info, Gang. I am now turning to this project.
BayesianGroupAna.py \
-dataTable $data \
-prefix gPPI.Bayesout \
-y beta -x part con \
-chains 4 -iterations 1000 \
-plot -more_plots rhat violin
What if I want to include some interactions?
My formula is:
beta ~ 1 + part + con + (1 | Subj) + (1 + part + con | ROI)
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dmoracze
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AFNI Message Board
Hi Gang - quick (hah!) question:
I have a complex task that I am calculating gPPI on 2 conditions, with the following event of interest structure:
ConditionA
initiation
outcome1
outcome2
ConditionB
initiation
outcome1
outcome2
At the individual level, I am calculating seed to whole brain gPPI and I have 8 a priori regions of interest that I'd like to use your new Bayesian R
by
dmoracze
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AFNI Message Board
Hi Gang - we have been getting some weird and inconsistent errors with 3dMEMA recently. These errors happen for new analyses and old scripts that previously worked (and nothing was changed). Sometimes the program seems to work fine, however, many more times we are halted by random errors. I have tried to find a pattern and cannot. I can run the same code on the same data multiple times in a row a
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dmoracze
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AFNI Message Board
Thank you both! I'll let you know if either of these don't work.
by
dmoracze
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AFNI Message Board
Hello,
We have used R and matlab for the decoding of trial-wise beta values. We'd now like to take our 3D stat maps and convert them to visualize in AFNI. We are able to write AFNI datasets and combine the stat files. Currently, as an example, we have a 3D dataset where sub-brick 1 is a t value, sub-brick 2 is a z value, and sub-brick 3 is a p value.
The issue is that we want to use th
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dmoracze
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AFNI Message Board
Hi Rick,
Thanks for your response. I generated the padded time series exactly how you suggested and it looks right. However, for my 1st level analysis, the stats still look weird.
Here is my 3dDeconvolve command:
3dDeconvolve \
-input $runs -jobs 24 \
-polort A \
-ortvec MoPar_demean_pad.1D demean \
-ortve
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dmoracze
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AFNI Message Board
Thanks, Rick. I'll look into detrending as you suggest.
I have also gone a different route by mean padding the time series to appear continuous. You suggested this here.
As a proof of concept, I want to calculate a sound>no sound contrast using the padded time series. Previously in this thread you showed me how to generate this contrast by specifying my own design matrix using -ortv
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dmoracze
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AFNI Message Board
Hi Rick, I wanted to follow up.
As a reminder, I have ISSS data where participants hear a sound during a silent period, followed by 3 image acquisitions. I have 6 runs with 180 time points per run (which are not continuous). Previously in this thread I was trying to find the main effect of sound > no sound. My issue with the over specified design matrix was that I was coding the baseline vo
by
dmoracze
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AFNI Message Board
Hi Rick,
Thanks for your help on this. The reason that the design matrix was over specified is because I was also labeling the baseline volumes. I will change these to 0.
I have another question about this analysis:
I would like to calculate trial-specific betas using the LSS method in 3dLSS. However, from what I understand, 3dLSS can only be used if you specific a single -sitm_times_IM
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dmoracze
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AFNI Message Board
Hi Rick,
Yes that makes total sense. I'll investigate this further. Our GLM analysis is just to see if the paradigm is 'working'. However, our main analysis of interest is to generate TR impulse responses for each trial for MVPA.
Thanks,
Dustin
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dmoracze
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AFNI Message Board
Ok, this *seemed* to work and the results look as I'd expect. However, I had to use a -GOFORIT 4 to get it to run, which makes me nervous so I'd like to confirm with you.
The design matrix includes:
columns 0 - 23 - polort
columns 24 - 35 - motion and derivatives
columns 36 - 47 - impulse response matrix as formatted in my previous post
Relavant columns for my example:
36 - 38
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dmoracze
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AFNI Message Board
Hi Rick, thanks for the response.
As you can imagine, I was trying to sidestep using the old fashioned way! The only reason I thought that this might work is due to this line in the help file:
*N.B.: The q-th column of 'fff' will get a label
like 'lll' in the 3dDeconvolve results.
I will try as you say, thanks for the input!
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dmoracze
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AFNI Message Board
Hello,
I'd like to create an impulse response model. My functional data are not continuous (e.g. sparse) and thus it is not appropriate to insert stimulus timing files. For example, my timing files begin at the beginning of the experiment, but the functional data are not continuous. So if I use TENT or CSPLIN then it would take the timing file and generate my impulses accordingly, except
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dmoracze
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AFNI Message Board
Candidates are being considered for a postdoctoral research associate position as part of a collaborative project between Dr. Luiz Pessoa’s Laboratory of Cognition and Emotion (http://lce.umd.edu/) and Dr. Elizabeth Redcay’s Developmental Social Cognitive Neuroscience lab (http://www.dscn.umd.edu) at the University of Maryland, College Park. The postdoc will be primarily involved in studies to ex
by
dmoracze
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AFNI Message Board
The University of Maryland Developmental Social Cognitive Neuroscience Lab directed by Dr. Elizabeth Redcay (www.dscn.umd.edu) is seeking a full-time Technical Research Assistant (formal title: Faculty Assistant) beginning late Spring or early Summer 2017. The DSCN lab investigates the neural and cognitive bases of typical and atypical development, with a focus on social cognition and social moti
by
dmoracze
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AFNI Message Board
Hi Gang,
I am running 3dLME on 24 subjects with repeated measures (2 conditions per subject), thus 48 datasets. The input file for each dataset consists of one z value per node and I am using std.60 standardized mesh (36,002 nodes per hemi). Here is a schematic of my command:
$h equals hemisphere (looping over lh and rh)
3dLME -jobs 24 \
-prefix LME.int-
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dmoracze
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AFNI Message Board
Hello,
I am a little confused by the suggestions here, but maybe I am not getting something. My ISSS sequence is 3 volumes followed by 1 silent volume. So I need to zero pad my time series so that after every three volumes, I insert a zero or mean volume. Obviously I will need to pad my regressors accordingly.
1) How can I quickly generate the censor file using AFNI tools? I essentially n
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dmoracze
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AFNI Message Board
The Developmental Social Cognitive Neuroscience lab at the University of Maryland has an opening for a postdoctoral fellow. This position is supported by an NIMH-funded grant investigating how brain network organization contributes to atypical social interaction in autism spectrum disorder. Research in the lab is focused on understanding the role of social-cognitive and motivational brain network
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dmoracze
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AFNI Message Board
Bump. I'm still concerned about this issue. Thanks for any help.
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dmoracze
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AFNI Message Board
Hello, I am also interested in this. Does anyone have any further recommendations other than what Rick previously suggested?
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dmoracze
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AFNI Message Board
Hello, this is primarily to ease my troubled mind:
Say I have multi band data with the following slice time acquisition:
> 3dinfo -slice_timing mydata+orig
0.000000|0.685000|0.112500|0.797500|0.227500|0.912500|0.342500|1.025000|0.455000|1.140000|0.570000|0.000000|0.685000|0.112500|0.797500|0.227500|0.912500|0.342500|1.025000|0.455000|1.140000|0.570000|0.000000|0.685000|0.112500|0.797500
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dmoracze
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AFNI Message Board
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Pages: 123