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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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Thank you Daniel and Rick for the help
1. Simple ROIstats just on the Coef sub-briks of the stastistical output of the tasks, and modeled baselines.
3dROIstats -mask $mask1 $top_dir/Processing/simic_results_12_Linux/$subj.results/stats.{$subj}_REML+tlrc.HEAD'[1,4,7,10,13,16,19,22]' > $results_dir/$trial.$subj.txt
2. The *_baseline.1D timing files are representative of all
by
John
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AFNI Message Board
Hello Daniel,
each subject is doing an Nback Task, with a single run for each. The task is just a repeating set of stimuli; baseline, announce, task for 9 repetitions, and 52 subjects.
Almost all of the run is modeled by the given blocks.
The mask I used is an ROI from the PCC.
Thank you for the assistance
afni_proc.py -subj_id $subj -script proc.5.23.$subj -scr_overwrite
by
John
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AFNI Message Board
Looking at 3dROIstats results on beta coefficients i've noticed a lot of my subject's 3dDeconvolve stats outputs will have negative values across nearly their entire run.
IE I've modeled all most all over the run ~95% and for a given mask its average seems to always be negative after regression when looking at the beta values of a BLOCK.
In same Default mode network masks th
by
John
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AFNI Message Board
I just have a few questions regarding building the Interaction stimuli for the last run of 3dDeconvolve. I pulled my seed time course from "clean data" that I created using Gang's process using 3dSynthesize, and 3dCalc described in his procedures for simple correlation.
Few questions;
1) I would assume the seed time course with effects of no interest removed would be acceptabl
by
John
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AFNI Message Board
Hello,
I have a few questions regarding the simple correlation method as well so i'll piggyback this subject somewhat
I have data from a task related experiment, and have previously used the PPI/Context Dependent Correlation methods discussed on Gang's website. For using the older simple correlation analysis method w/fim+ and task data what might be the most appropriate way to
by
John
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AFNI Message Board
I'm looking for a bit of clarification/help using the PPI-Pipeline from here
For starting the PPI pipeline I should not use 3dDetrend initially but instead use 3dSynthesize on my input dataset to making a dataset of my baselines/regressors of no interested then use 3dcalc to make a timeseries with those removed? I would believe this covers the detrending as my polorts were removed as eff
by
John
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AFNI Message Board
Hello,
I was wondering about the region selection for whereami. I wanted to remove certain regions from my masks using 3dcalc and the whereami atlas functions. Many of these regions span across multiple atlas indices, and wondering about the input parameters for whereami in the "-mask_atlas_region" input. If a name is entered the program will suggest and give an index number correspo
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John
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AFNI Message Board
I believe i understand. the errts.anaticor file is shorter. I don't know enough about the anaticor process, apart from its white matter regression, and the residual's vary over voxels.
From looking at the header files I understood 3dTfitter was removing the TR's and reading the from the ANATICOR Summary
"What @ANATICOR does (6) : Regression by “3dTfitter” with voxel-wise
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John
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AFNI Message Board
Ah thank you for the comprehensive walk through and commands. I failed to look originally at the errts.$subj files which do indeed contain the censored TR's, with zero values. I had orignally picked the errts.anaticor.$subj 3d+time file which does seem to just do away with TR's, which makes sense since its primarily for resting state, where time continuity is less important?
I'l
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John
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AFNI Message Board
Hello,
I'm interested in doing some analysis on errts datasets created after preprocessing. I'm interested in using specific blocks designated by the task in the scanner via ideal.$task.1D files. Using 3dTcat to concatenate certain blocks over a scan for analysis is problem free with unprocessed 3d+time files as no TR's have been censored but after preprocessing there are of cou
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John
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AFNI Message Board
"pain_ratings.txt file type: UNIX
pain_ratings.txt has 0 bad characters"
by
John
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AFNI Message Board
I'm still receiving the error message "** Error:
Failed to read matrix from /Users/gracelyjl/Documents/local_john_may/scripts_list/pain_ratings.txt "
using the same covariate file previously posted.
in the same script as above but with only 1 set, using the Coef + T-stat briks of the glt.
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John
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AFNI Message Board
Hello Gang,
Thank you for the suggestions. If I use the contrasts of the conditions, may I then use the covariate file?
Thank you,
John
by
John
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AFNI Message Board
Hello,
I'm been having trouble introducing covariate files to my 3dMEMA scripts. The scripts previously ran without any issue, so I assume there must be something i'm overlooking regarding the covariates. The other question I have is the choice between selecting "-groups set 1 set" vs "-conditions set 1 set 2" this is in regards to whether the groups being compar
by
John
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AFNI Message Board
I'm also interested in looking at MSSD variability through 3D+T images but was wondering if I could do so after 3dDeconvolve via afni_proc.py as I'd like to preprocess the data in a similar fashion to resting state data such as the afni_proc.py example #9b using anaticor.
I'm interested in the mean variability during different blocks, but am curious as to whether using "3dc
by
John
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AFNI Message Board
Hello,
I was wondering might be the best way to go about creating a gray matter mask now. The topic was brought up a few years ago, but I wasn't sure what might be the most up to date way now whether its Draw ROI plugin or Gyrus Finder, or NIMH's ROI Builder tool. Another very simply question was drawing on a Mac OS. I recall I had to hold something or change something when using the
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John
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AFNI Message Board
Hey Isaac,
Thank you for the comprehensive response. I'm currently on Mac OS 10.7. I believed I installed the mac package I found from the numpy website, it required python 3 which I just use infrequently with a different alias. Quick couple questions. Are there environment or path's I have to set to use Numpy? I didn't read anything of it and the installer did not change my var
by
John
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AFNI Message Board
Isaac,
This is very helpful for converting -CENSOR TR files to external -censor files. Do i simply add the Numpy Package to my existing Python Library? I'm not too familiar with Python programs apart from coming across them in AFNI.
Thank you,
John
by
John
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AFNI Message Board
Hello,
I was wondering what might be the best way to go about a comparison between a patient group and control group, the results of an intra-group/inter-subject paired t-test. Here is my deconvolution parameters from the afni_proc.py I used on 50~ subjects.
-regress_stim_times \
$stim_dir/zed_pretiming.1D
by
John
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AFNI Message Board
Daniel I used align_epi_anat.py with the final output of functional images from afni_proc.py before deconvolution/regression and the alignment results seem to be very good. When using afni_proc.py, 3dcopy is importing my .nii files immediately into +tlrc automatically. So it won't tlrc warp within afni_proc.py.
Rick I'm going to follow your suggestion and run 3dcopy, 3drefit -view, 3
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John
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AFNI Message Board
I think it was purely due to poor warping. I've been testing various ways to warp/normalize across the subjects before group comparison and am still having poor results getting my EPI's aligned properly with their respective normalized anat's.
Here is what I'm currently doing, and seems to be the most common way I've come across warping so far (I did use afni_proc.py,
by
John
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AFNI Message Board
Hello,
I'm a relative newbie to AFNI group analysis coming from SPM. I have a dataset of subject functional runs (1 Func/subj) that were originally converted to .nifti format from their raw P files, and that is where I've started, the raw files are no where to be found. When I originally started using 3dcopy to convert to .BRIK/.HEAD, AFNI was echo'ing the warning about obliquit
by
John
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AFNI Message Board
Hello, I figured I would piggyback off this issue
Having issues with 3dDeconvolve -stim_times in my block design.
my 3dDecon.err files says
"** ERROR: 'BLOCKS' has illegal power: only 4 or 5 allowed
** FATAL ERROR: '-stim_times 1': don't understand basis function model 'BLOCKS(25,1) '
~
by
John
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AFNI Message Board