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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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Here is the script. I ran a paired ttest between two conditions and included a covariate.
3dttest++ -prefix /imaging/Analysis/Ttest_Feb2022/FeelvsNat_Neg -paired \
-setA Feel_Neg \
1422 /imaging/1422/1422.results/Feel_Bad_Resp+tlrc.BRIK \
1423 /imaging/1423/1423.results/Feel_Bad_Resp+tlrc.BRIK \
1425 /imaging/1425/1425.results/Feel_Bad_Resp+tlrc.BRIK \
1426 /imaging/1426/1426_giantmove.r
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tamtam
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AFNI Message Board
Thank you.
Is there a specific threshold that can be used to identify whether a participant should be removed from the analysis? I am wondering whether one of my participants is highly influential. In a normal regression, I would use Cook's D or leverage values to identify these cases, but not sure what the standard is with AFNI.
Thank you
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tamtam
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AFNI Message Board
HI there,
I was wondering whether AFNI has any influential diagnostics statistics that can be ran after completing a paired t-test using 3dttest++ to identify influential participants?
Thank you,
Tamara
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tamtam
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AFNI Message Board
Hello,
I would like to verify my interpretation for the paired 3dttest++ output when I include a covariate.
For subbricks that include a covariate (e.g., sub-brick 2 and 3 in the example below) do these show clusters representing differences between SetA and SetB while holding covariate IQ constant? OR would you interpret the significant clusters as differences between SetA and SetB for d
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tamtam
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AFNI Message Board
Hello,
I created my afni.proc script based on examples I saw on the afni website. I have ran this script on my participant's and it runs successfully. I have checked the QC html and the outputs seem good. I have two questions based on my script and QC I am planning on doing:
(1) I was wondering whether my script looks okay and whether there is anything integral missing or anything else
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tamtam
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AFNI Message Board
Hello,
I ran 3dMVM (code below), and although I got an output I received the following warning message and I am not sure what it means and whether I need to do something. Any suggestions or comments would be greatly appreciated!
Thank you very much,
Tam
3dMVM output:
++ Smallest FDR q [0 (Intercept) F] = 6.39594e-13
*+ WARNING: Smallest FDR q [1 group F] = 0.702769 ==> few true s
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tamtam
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AFNI Message Board
Thank you very much. I have these remaining errors when I attempt to install the R packages for AFNI (see below last parts of the output).
Apologies for the novice questions, but are these errors specific to R or is there something within the AFNI installations I can do? I tried to uninstall and re-installed R, but I am still getting this problem. I have also included the output for the afni_ch
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tamtam
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AFNI Message Board
Hi there,
I checked for AFNI updates and a message appeared indicating that I did not have the relevant R packages installed (I had everything previously). I ran "rPkgsInstall -pkgs ALL" and it seems like it could not be installed properly. I was wondering whether you have any solutions to these errors am receiving?
Thank you,
Tamara
TERMINAL OUTPUT
ttavare@MitchellLabImage
by
tamtam
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AFNI Message Board
Hello,
I would like to incorporate the -big_move function to help align my epi and anat data better, though I am not sure where I should include this option in my script. Any help is appreciated!
Thank you,
Tamara
afni_proc.py -subj_id 1423 -script proc.big_July_2021 -scr_overwrite -blocks \
tshift align tlrc volreg blur mask scale regress -copy_anat \
/imaging/Tamara/Youth/
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tamtam
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AFNI Message Board
Hello,
We have a participant who completed an anatomical, 2 epi runs and then unfortunately, had to be removed from the scanner. Shortly after, the participant went back in to complete the remaining 3 runs and completed another anatomical.
I was wondering whether there is a way to salvage and possibly use this data? Can I average the two anatomical scans and align all the functional runs to
by
tamtam
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AFNI Message Board
Hello,
We have a participant who completed an anatomical, 2 epi runs and then unfortunately, had to be removed from the scanner. Shortly after, the participant went back in to complete the remaining 3 runs and completed another anatomical.
I was wondering whether there is a way to salvage and possibly use this data? Can I average the two anatomical scans and align all the functional runs to
by
tamtam
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AFNI Message Board
Hi there,
Regressor files are organized in the following format in seconds: ONSET: DURATION. The duration of the events in each regressor should be the same, though sometimes there are very slight variations in the duration times (milliseconds) due to computer processing variations, so I wanted to specify the duration times in the regressor to model the events as accurately as possible.
Fo
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tamtam
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AFNI Message Board
I tried the second command without the hyphen...
ttavare@MitchellLabImage:/imaging/Tamara/Youth/1423$ cat ls l /imaging/Tamara/Youth/1423/Instruct.txt
cat: ls: No such file or directory
cat: l: No such file or directory
.4: .9 18.6: .9 35.9: .9 56.1: .9 73.4: .9 89.6: .9 107.9: .9 131.6: .9 151.9: .9 168.1: .9 191.9: .9 209.1: .9 225.4: .9 248.1: .9 266.4: .9 283.6: .9 301.9: .9 3
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tamtam
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AFNI Message Board
Thank you very much for your response. I could only get an output for the first command, the other one did not work (see output below)
ttavare@MitchellLabImage:/imaging/Tamara/Youth/1423$ ls -l /imaging/Tamara/Youth/1423/Instruct.txt
-rw-r--r-- 1 ttavare domain^users 1092 Dec 6 21:09 /imaging/Tamara/Youth/1423/Instruct.txt
ttavare@MitchellLabImage:/imaging/Tamara/Youth/1423$ cat ls -l /im
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tamtam
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AFNI Message Board
I should also indicate that I also ran the " -prefix FIXED.txt" option, and I received the same error message when I used the "fixed" stimulus file.
Thank you very much for your help.
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tamtam
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AFNI Message Board
Hi there,
My afni_proc.py file is having difficulty with opening one of my stimulus files.
When I ran the file_tool code, it indicated there were no "bad characters". Any other suggestions I can try?
Thank you very much
file_tool -test -infile Instruct.txt
Instruct.txt has 0 bad characters
Instruct.txt file type: DOS
consider: file_tool -show_file_type -infile Instruct.t
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tamtam
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AFNI Message Board
My apologies, I had edited an older version of the full script. I have included the afni.proc.py I just created below with the parameters I think are "good" for my study.
Thank you again!
# afni_proc.py -subj_id 1423 -script proc.Dec5_2020 -scr_overwrite \
# -blocks tshift align tlrc volreg blur mask scale regress -copy_anat \
# /imaging/Tamara/Youth/1423/1423.anat
by
tamtam
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AFNI Message Board
Thank you very much for your suggestions.
I have included my AFNI script below. For my regressors with no timing information (i.e. participants did not respond), I have included "-1:1" in the regress file.
One question I have is what (1) what stim_time and (2) stimulus basis functions I should use? Here is some additional information about my stimuli and regressors:
-My stimuli
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tamtam
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AFNI Message Board
Thank you very much.
I did edit this script from a previous one I had written a bit ago since I wanted similar parameters. I figured that the problem was that I had entered the wrong " ' " in the regress block -a consequence of me editing the script.
When I tried to run my script again, I recieved the following message:
*+ WARNING: '-stim_times 1' didn't
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tamtam
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AFNI Message Board
Hi there,
I am receiving this error message when I try to run my pre-processing script (see below). I don't see any additional spaces in my script. Any suggestions would be helpful!
Error Message in Output Script
3dTstat -prefix rm.mean_r02 pb03.1423.r02.blur+tlrc
++ 3dTstat: AFNI version=AFNI_20.3.02 (Nov 12 2020) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output datase
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tamtam
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AFNI Message Board
Thank you very much for your quick response! I will try to create a pre-processing script using the examples online.
Thank you for your feedback.
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tamtam
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AFNI Message Board
Hi there,
I am trying to set up my pre-processing script using the uber_subject.py, though, when I attempt to run this command, I received the following message:
**** failed to import PyQt4.QtGui ****
PyQt4 must be installed to run the uber_subject.py GUI
--> see the output of: uber_subject.py -help_install
Reading other posts, it seems like uber_subject.py is no longer rec
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tamtam
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AFNI Message Board
Hi Gang,
Sorry, I was able to figure out the issue just now. Thank you again for your help.
In your previous message, you had suggested that I include the VBM in the between subject line in the model with the assumption that the VBM values do not vary within subject. I just want to clarify whether it would be appropriate it include the VBM values in the bsVars line or the Wsvars line.
T
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tamtam
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AFNI Message Board
Thank you very much!
When I now try to run the code, it keeps telling me "3dMVM: No match" . This code had worked previouslty. Do you know why this error keeps coming up?
Thank you,
Tamara
by
tamtam
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AFNI Message Board
Hi there,
I included the the SPM/VBM grey matter output as a voxel-wise covariate in the ANOVA (3dMVM). After I ran the anova with the covariate, I didn't see any differences in the output relative to when no covariate was included. Below is the code I used. There were no error messages. Does this code look correct?
Thank you very much.
Code:
3dMVM -prefix Choice_VBM -jobs 4
by
tamtam
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AFNI Message Board
Hello,
I was wondering how I can check the orientation of a volume. I have been using 3dinfo for this and looking at the [-orient xxx].
When I looked at the orientation of one of my images it was ASR. Then I used 3dLRflip (3dLRflip -LR -prefix New volume OLD Volume) to double check the orientation of the volume. After I ran 3dLRflip the new image was still ASR. Shouldn't the orientati
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tamtam
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AFNI Message Board
Dear AFNI,
How do I find out whether my images are in different orientations? I am interested in using my VBM output file as a covariate in my 3dMVM. Prior to running the 3dMVM with the VBM covariate I used 3dresample to change the voxel size of my VBM files to match the voxel size of my stats file (changed 1x1x1 to 2x2x2). After running this, I recieved the following error message:
Error i
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tamtam
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AFNI Message Board
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Pages: 123