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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
Page 2 of 3
Pages: 123
Results 31 - 60 of 65
Hello,
I am generating individual trial-wise beta estimates for functional connectivity analysis (a la Rissman, 2004) but I am interested in estimating response based on Mumford 2012. Thus, I have been using 3dLSS. My question is:
How do censored TRs affect the trial-wise beta estimate output from 3dLSS?
I am generating my design matrix with exactly one -stim_times_IM in Deconvolve. I al
by
dmoracze
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AFNI Message Board
Developmental Social Cognitive Neuroscience
Lab manager/Research Assistant Position
Psychology Department
University of Maryland, College Park
The University of Maryland Developmental Social Cognitive Neuroscience
Lab directed by Dr. Elizabeth Redcay (www.dscn.umd.edu) is seeking a
full-time lab manager starting this summer 2016. The DSCN lab
investigates the neural and cogniti
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dmoracze
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AFNI Message Board
Hello,
I am wondering if the autocorrelation function (-acf) that was added to 3dClustSim, 3dblurtoFWHM, and 3dFWHMx could also be added to their surface-based analogues (SurfClust, SurfSmooth)? I assume the autocorrelation issue would be present in both volume and surface data. I looked through the update history and couldn't find this update so please let me know if this option is alrea
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dmoracze
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AFNI Message Board
Thanks, Rick.
I can dump the node-wise time series and calculate the whole-brain mean in R. I was just checking if there was an easy way to do this in afni. Thanks though.
Dustin
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dmoracze
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AFNI Message Board
Hello -
I am doing analysis on the surface and would like to extract the mean time-series from a bilateral ROI. My surface data and ROIs are divided by hemisphere, but I would only like one mean time-series in the end. I can think of a few convoluted ways to go about this, but is there a quick way extract the mean of a ROI from both hemis in one step?
Thanks,
Dustin
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dmoracze
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AFNI Message Board
Yes, round-a-bout way indeed but I just needed to do the same thing and I had the help of a friend who suggested I try and find the border nodes:
Perhaps there is a better way do to this, if anyone has any suggestions it would be helpful. I wrote these out to be explicit but it would be easy to nest and loop for less code.
In matlab:
roi = import(roi_file.1D); % import roi
% assuming t
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dmoracze
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AFNI Message Board
This seems like a round-a-bout way, but could you use SurfPatch to convert the ROI nodes into a surface patch, then use SurfaceMetrics to find the boundary_nodes, then set all of the boundary nodes to 0. Then repeat this procedure for however many nodes you wish to erode?
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dmoracze
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AFNI Message Board
Thanks, Rick! Censoring was the culprit. If I do -allzero_ok will the result only be betas that it could predict based on this matrix or will anything be interpolated?
Ex. if I had 24 trials on a run, but column 24 is all 0s, will the IM_censored matrix created with -allzero_ok preserve this time scale such that the input -data into 3dLSS will properly align with -matrix? And will the out
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dmoracze
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AFNI Message Board
Hello -
I am trying to generate beta estimates for each trial using stim_times_IM, I'll then take the design matrices to 3dLSS for the betas. However, I have a couple of subjects who fail at the matrix creation because some of the events have an "all 0" column. If I have a
timing file with event onset:duration and I want to generate a beta for each event, how can one of those
by
dmoracze
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AFNI Message Board
My attempts to run this on my server failed with the above command. I tried to run the stripped down command that I uploaded to your server on my local machine and got a different error:
Z slice # 1 done: 08/13/15 19:40:09.605
[1] "Analysis finished: 08/13/15 19:40:09.682"
[1] "#++++++++++++++++++++++++++++++++++++++++++++"
outLabel adult:b adult:t kid:b kid:t kid-adul
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dmoracze
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AFNI Message Board
Thank you. Files uploaded
On a related note, I am having problems with 3dMEMA for another project as well. This is just a one sample group map of a task-based contrast. The error I am getting is this:
Error in abs(x) : Non-numeric argument to mathematical function
Calls: mapply -> <Anonymous> -> ifelse
Execution halted
Any idea what could cause this? Thanks!
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dmoracze
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AFNI Message Board
Hello,
I have 2 groups, kids and adults in my surface-based analysis stream. For each group I have 6 stats files per subject. These stats files correspond to 6 seed-to-whole-brain functional connectivity maps. I would like to compare whole brain connectivity of each seed regions across groups. Thus, I would like the results of this step to be 6 stats files corresponding to kid-adult for e
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dmoracze
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AFNI Message Board
Hello - I have a large design matrix because I have specified a CSPLIN(0,13,14) response model. Using ExamineXmat I like how I can look at subsets of the matrix, but I was wondering if it is possible to see the r values in these subsets instead of the heat map color? I searched for a way to subset the correlation matrix using 1d_tool and found nothing (perhaps I didn't look hard enough).
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dmoracze
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AFNI Message Board
Yes, that was my fault for making the assumption that cat_matvec would work properly regardless of the file extension. I was copying the afni_proc script that was the base for my script into this thread, but I had changed the naming conventions in my batch script to reflect my own naming preferences. Sorry for the confusion but thanks for the help.
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dmoracze
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AFNI Message Board
Here is the output of the files in question. However, I figured out the problem. According to cat_matvec -help:
"The filename must end in the characters '.aff12.1D'"
I must have overlooked this when I was altering afni_proc to my batch script and my file just ended in .1D. When I change the file name to something that cat_matvec will recognize I get an output that I would
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dmoracze
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AFNI Message Board
Ok, thanks. Yes the mat file from 1Dmatrix_save does have one row per sub brick. However, I'm not sure how the frame to frame displacement is represented in the mat file created in the next cat_matvec step.
This is the volreg step from afni proc that I adapted for my batch script:
# ================================= volreg =================================
# align each dset to ba
by
dmoracze
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AFNI Message Board
Sorry for the confusion. I copied and pasted but removed subject and run identifying info in the warnings but not my batch script code. They are the same file.
If I did this right, the cat_matvec command is that same as the one created in afni_proc. This command gives me 1 row of 12 numbers and I'm not sure how this targets frame-wise displacement for each sub-brick.
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dmoracze
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AFNI Message Board
Hello - I tried to search for an answer to this question but couldn't.
I have edited an afni_proc output for batch processing, so my volreg step looks pretty much identical to
During the 3DAllineate step, I receive a lot of:
*+ WARNING: -1D*_apply 'sub002.warp.mat.1D': 1 isn't enough rows for source dataset -- last row will repeat
...
...
++ ========== sub-brick #11
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dmoracze
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AFNI Message Board
Hello,
I created a batch script for @SUMA_Make_Spec_FS. It ran properly for most of the 40-some subjects. However, it failed for one person. The orig mesh was created but during the creation of the standard meshes it failed. std.141 and std.60 was not created for lh surfaces.
This output is a clue, but I am not sure where to go from here:
Error MapIcosahedron:
Morph Surface lh.spher
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dmoracze
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AFNI Message Board
That makes sense.
Thanks so much for the thorough clarification!!
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dmoracze
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AFNI Message Board
Hello,
Why is there a difference between:
3dvolreg -maxdisp
++ Max displacement in automask = 0.55 (mm) at sub-brick 140
and
1d_tool.py -infile MoPar.1D -show_max_displace
max_enorm_diff = 0.403531
They aren't wildly different, but I'd like to be getting the same results from my motion quality checks.
Thanks!
Dustin
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dmoracze
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AFNI Message Board
Really cool stuff.
Is this option (as well as the output of correlation bricks) available in SUMA?
Also for AFNI and SUMA. I would love the option to overlay a mask on a correlation dataset and output mean correlations based on the mask. Like, if I had a mask with 2 ROIs, I could setup InstaCorr, overlay the mask, the drag the pointer around and settle on a seed region, then output mean c
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dmoracze
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AFNI Message Board
Hello,
How are the censored time points represented in the design matrix and the errts in 3dDeconvolve?
I would assume that the same would be true for the previous time point as well if censor_prev_TR were used in 1d_tool?
I ask because I am doing connectivity analysis on the errts after regressing motion, WM, and Ventricle signal and I want to understand how the censored time points are t
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dmoracze
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AFNI Message Board
Hello,
I am using the following to normalize:
-a data
-b mean
-expr 'a/b * 100'
I have tried 2 processing streams with different results:
1) slice time > volreg > co-registration > mean WM and LV extraction > nuisance regression > vol2surf > surfsmooth > intensity normalization
or
2) slice time > volreg > co-registration > intensity norm
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dmoracze
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AFNI Message Board
This is great!
Perhaps you plan on this but a number for the AFNI interface would be good similar to what you have for SUMA and FATCAT, especially outlining different plugins and options (i.e. instacorr)
Also, it would be nice to have a "What do you want to do?" type interface that outlines different programs and their general purposes. This may not be ideal because so many progr
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dmoracze
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AFNI Message Board
I can't delete my message, but I solved the problem.
@SUMA_AlignToExperiment -exp_anat <afni_T1> -surf_anat <SUMA>/SurfVol -align_centers -wd -prefix <prefix> -surf_anat_followers <SUMA>/aseg.nii
I guess I needed the -align_centers and -wd combo with the orig surf anat and aseg to follow...
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dmoracze
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AFNI Message Board
Hello,
I would like to use Freesurfer a surface / segmentation for processing in AFNI. I have run @SUMA_Make_Spec_FS.
I first want to use aseg.nii to create masks to regress out wm and ventricle signal. However, aseg.nii does not align with the T1 or epi AFNI datasets.
I have tried @SUMA_AlignToExperime -exp_anat <T1+orig created with to3d> -surf_anat <aseg.nii> -prefix <p
by
dmoracze
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AFNI Message Board
Page 2 of 3
Pages: 123