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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 37
Looking for wisdom on the AFNI x encryption interaction - Anyone noticed a change in script speed and output after encrypting? I'm getting a new computer up and running and would love some input on a security option that doesn't slow down large dataset scripts (if that's even a real concern)...
Any thoughts are appreciated!
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Noah
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AFNI Message Board
Thanks to you both. I can't seem to find the error here despite much work, having done both of the suggested steps here.
In case it was an issue of not having a column with data, I added the path to the data in the covariates file, but did nothing except changed the error a bit to include the Fatal Signal 11 at the end.
My error remains:
++ 3dttest++: AFNI version=AFNI_2011_12_21_1
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Noah
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AFNI Message Board
Thank you! Everything was pasted directly with no edits. I will investigate further.
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Noah
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AFNI Message Board
Good morning -
I am exploring the human connectome dataset with AFNI, doing standard seed-based connectivity to try to replicate some studies RSFC out there. At the end I'm using 3dttest++ to display some ttests vs. zero for my seed of interest, while I'm attempting to covary for age and gender.
My 3dttest++ script file is set up like so:
100307 /Volumes/Faraday/DATA/DBS_RSFC/10
by
Noah
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AFNI Message Board
Thanks Paul. 3dExtrema seems to be the best route - however, am I correct that it kicks out all the maxima within the ROI mask?
The command was: 3dExtrema -volume -closure -mask_file ../mask+tlrc $name_Z+tlrc
Maxima for Volume #0 (Coordinates Order = RAI):
Index Intensity RL AP IS Count Dist
----- --------- ------ ------ ------ ----- --------
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Noah
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AFNI Message Board
Thanks Rick, that was precisely what I was looking for (and apologies for the late thank you).
by
Noah
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AFNI Message Board
Good morning AFNI folks and thanks in advance for your help.
I'm looking to plot the bivariate between peak Z scores of connectivity obtained in my experiment, with a behavioral variable (in SPSS). Is there a way to extract only peak Z score, within an ROI, without taking the average? I've read through the -helpfiles for 3dmaskave and 3dmaskdump and don't quite see what I
by
Noah
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AFNI Message Board
Thanks for the quick response Rick.
The larger picture is that I am interested in exploring how two patient groups differ in global-based connectivity (3dTCorrMap), and want to evaluate each voxel's connectivity with "all other voxels," ensuring that voxels identified belong to gray matter, independently based on Freesurfer gray matter maps.
One approach (the original post
by
Noah
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AFNI Message Board
Good morning AFNI gurus - couple questions for you. I am trying to use freesurfer grey matter for my anatomical dataset for preprocessing.
afni_proc.py command is:
afni_proc.py -subj_id $name \
-script proc.$name -scr_overwrite \
-dsets $name/$name.rest1+orig.HEAD $name/$name.rest2+orig.HEAD\
-copy_anat /Volumes/Faraday/DATA/ELS_Pilot/$name/$name.fre
by
Noah
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AFNI Message Board
Hello AFNI gurus - question about using Clustersim and its application to segmented data.
I often use segmented data (via AFNI, freesurfer, etc) for my FMRI analysis and then run clustersim on the resultant matrix. As I was doing this, I realized that my "grayordinate space" (i.e., segmented space) is actually quite smaller than the three dimensional matrix specified in clustersim.
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Noah
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AFNI Message Board
Thanks - another question @ GangC et al.
I am still looking at genotype status on RSFC from a given seed. I've evaluated base pair length as a covariate, but now I am curious about an interaction between base pair length in one gene and the base pair length in another (or similar idea).
Can ttest++ handle that operation? Or is this an opportunity for me to learn 3dMEMA? Other app
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Noah
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AFNI Message Board
I meant graphically, but I can easily change the colors. Thanks for your help!
by
Noah
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AFNI Message Board
Thanks for the clarification Gang. While I am thinking about it, is there a way to display it as negative linearity?
Much appreciated,
Noah
by
Noah
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AFNI Message Board
Hello AFNI gurus - quick question for you.
I am covarying my seed-based connectivity imaging results by genotype status, in this case by # of base pairs (i.e., a continuous variable, with range from n to n + some much larger bp number). When I am reading the imaging outpt, some areas demonstrate more connectivity, others less etc etc.
When I see an area has increased connectivity, what is
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Noah
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AFNI Message Board
Absolutely want to evaluate rsfc and betas separately at the group level- that's the final goal.
I think I was unclear; my apologies. Each participant has one beta and one z-score.
by
Noah
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AFNI Message Board
Thanks Gang, happy to oblige.
1) Each group has roughly the same subjects (plus or minus one per group)
2) There are two separate imaging runs, ie resting state and emotional processing
3) exposure also has two levels. Within each group there are not between subject variablity
4) I have Z scores for the rsfc and betas for the emotional processing.
N
by
Noah
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AFNI Message Board
Hello AFNI gurus - I have a data analysis question.
I am looking to look at the effect of genotype status (3 categories, ie 2 homozygous and 1 heterozygous) on imaging results, (i.e., resting state functional connectivity and emotional processing), within a sample that is divided by exposure status (i.e., a simple yes/no). This is my first time working with this kind of data and I am not sur
by
Noah
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AFNI Message Board
Apropos previous topics on the use of blurring, could you add a -blurtoFWHM option in RSFC? Right now there is just -blur fff.
Thank you!
Noah
by
Noah
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AFNI Message Board
Hello AFNI folks - I need some help.
I am trying to compare 2 ROIs (one functional, the other structural) and evaluate their overlap. How would I do this in AFNI? I see the example #9 in 3dCalc's helpfile, but I was hoping to be able to generate some quantitative metrics (i.e., % overlap, etc).
Any suggestions? Thank you in advance.
by
Noah
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AFNI Message Board
Good afternoon -
I am getting the following error trying to perform a simple correlation with 3dDeconvolve. Aside from this error 3dDeconvolve is working (i.e., no matrix errors etc)
*+ WARNING: Input polort=2; Longest run=450.0 s; Recommended minimum polort=4
My run lengths are 180 TR, so I am not sure where the 450 seconds are coming from. The scripting is:
3dDeconvolve -polort 2 -i
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Noah
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AFNI Message Board
Thanks Ziad. I'll look forward to the pubs. Thanks for all you guys do.
by
Noah
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AFNI Message Board
As the AFNI gurus are no doubt aware, the Neuroimage article by Power et al 2013 (Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion) has caught a lot of attenion from reviewers and various Program folks. How does the censoring in afni_proc.py correspond to the steps suggested by the Power article? I see the -regress_motion and -regress_outlie
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Noah
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AFNI Message Board
Would this same logic apply if one used 3dTcat prior to correlation for resting state runs?
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Noah
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AFNI Message Board
Good morning AFNI experts - thanks in advance for some more help.
I have been running afni_proc.py for preprocessing of resting state analysis. Two of my subjects are coming back with this error, and I am not sure how to interpret it.
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=2.51095
* 9 singular values are less than cutoff=2.51095e-07
* Implies strong colli
by
Noah
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AFNI Message Board
is there a way to estimate the smoothness of residuals associated with the ReHo process itself? Otherwise I'm using smoothness of the signal, rather than noise.
by
Noah
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AFNI Message Board
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