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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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I've tested the code and this is the output displayed in the Terminal window (below). The resulting rs_errts image looks fine, but I am wondering if additional processing is necessary? For example, executing the 3dREMLfit command?
++ 3dDeconvolve: AFNI version=AFNI_21.0.00 (Jan 7 2021) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset rs_f.nii
++ Skipping check for i
by
Alfonso Alfini
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AFNI Message Board
Dear AFNI Experts,
I have inherited SPM-preprocessed EPI images for a resting-state analysis. These images have already undergone bandpass filtering, but NOT the removal of other nuisance regressors. I have the following text files (.txt) for each participant containing the 1) motion parameters, 2) global white matter signal, 3) global CSF signal, 4) global brain signal, and 5) censored TRs.
by
Alfonso Alfini
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AFNI Message Board
Dear AFNI,
I am working with arterial spin labeling data and each dataset contains a series of interleaved control and labeled volumes (e.g., C,L,C,L,C,L,C,L,C,L,C,L...). Because the mean signal intensity of the control and labeled volumes is different, the signal appears zig-zagged - which makes motion correction difficult. I would like to use 3dvolreg to perform motion correction of the con
by
Alfonso Alfini
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AFNI Message Board
Hello,
I am wondering if 3dLME has a -resid option like 3dttest++ to output residuals into a dataset? If not, is there another suggested way to obtain this?
Thank You,
Alfonso
by
Alfonso Alfini
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AFNI Message Board
Yes, you are right Rick! That explains it, there was not enough space left on that hard drive.
Thanks,
Alfonso
by
Alfonso Alfini
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AFNI Message Board
All of the unreadable output files were stored as .HEAD. It may have been the hard drive the images were stored on, after transferring to a different drive and rerunning the script, the new output files are now readable.
by
Alfonso Alfini
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AFNI Message Board
Hello,
I have recently used proc.py for a task related analysis. Inside my "results" directory I have a number of output files, as expected. However, when I use 3dinfo or try to open these files through command line, they cannot be read/opened. Additionally, when I try to view these files with the AFNI viewer (e.g. anat_final, mask_group, ect.) they do not appear as choices in the o
by
Alfonso Alfini
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AFNI Message Board
Thanks for the response Gang. I tried a few thresholds, but in the end decided to go with the 100% option.
Alfonso
by
Alfonso Alfini
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AFNI Message Board
Hello,
I am working with a dataset that has partial coverage. I am now ready for the group analysis, and although alignment and normalization worked pretty well, there is still some variability in how the epi maps overlap. I would like to use the -zskip option in 3dttest++ and I see I can put a decimal fraction after the option to indicate what percentage of voxels in each set must be nonzero
by
Alfonso Alfini
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AFNI Message Board
Hi Gang,
I've been working with Rick to figure out why I am getting the error below when I try to run 3dLME.
Reading input files now...
** Error:
At least one of the input files has different dimensions!
Run "3dinfo -header_line -prefix -same_grid -n4 *.HEAD" in the directory where
the files are stored, and pinpoint out which file(s) is the trouble maker.
Rep
by
Alfonso Alfini
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AFNI Message Board
Hello Afni Experts,
I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
P
by
Alfonso Alfini
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AFNI Message Board
Hello Afni Experts,
I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
P
by
Alfonso Alfini
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AFNI Message Board
Hello Afni Experts,
I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
P
by
Alfonso Alfini
-
AFNI Message Board
Hello Afni Experts,
I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
P
by
Alfonso Alfini
-
AFNI Message Board
Hello Afni Experts,
I used proc.py to generate a stats+tlrc image from a task based experiment. I am trying to use 3dLME for my group analysis, however when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
P
by
Alfonso Alfini
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AFNI Message Board
Hello Afni Experts,
I am trying to use 3dLME for a my group level analysis. However, when I execute the script I get the following feedback:
255a-280:3dLME_2.13.16 EGI$ ./step2.group_LME.sh
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
Package phia loaded successfully!
Warning message:
package ‘car’
by
Alfonso Alfini
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AFNI Message Board
Hello,
We have been using AFNI on a Mac computer in our lab for about three years. Recently we moved the Mac to a different room and have continued using it for preprocessing with AFNI. However, since the move the AFNI GUI/viewer won't open when its called (typing "afni" in the command line). Other AFNI commands still work. In an attempt to remedy the issue we updated AFNI with
by
Alfonso Alfini
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AFNI Message Board