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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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Great, thank you very much.
Just thinking about another possibility as I wait for SPM to get back to me....would I be able to convert the GM probability maps into talairach space using 3dwarp and then convert into the MNI 2009c template, or would this be too many conversions?
Thank you very much.
Tamara
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tamtam
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AFNI Message Board
Thank you very much!
If the GM maps are in a different MNI space, would it be possible to convert it into the MNI asymmetric 2009c version using 3dwarp?
Thank you,
Tamara
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tamtam
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AFNI Message Board
Hello,
I am hoping to include a covariate in my ANOVA to account for group differences in grey matter volume at the voxel-wise level. Specifically, I used the CAT12 toolbox in SPM to obtain voxel-wise grey matter probability maps for each of my participants and I would like to include these as covariates in my ANOVA (3dMEMA). This way I can control for atrophy in a finer scale versus using the
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tamtam
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AFNI Message Board
Hello,
I am interested in manually selecting ROIs based on atlases in AFNI. I aligned my subject's anatomical files using SSwarper and used the MNI152_2009_template_SSW.nii.gz template. With this, does it make sense for me to use the "TT_Daemon" atlas for segmenting the ROIs? If so, would I need to complete resolution conversion using 3dfractionize or 3dresample?
Thank you ve
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tamtam
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AFNI Message Board
great, thank you very much.
In this case, would it be incorrect to use glt with 3 factors? The example for "-glfCode K CODING" section in the AFNI 3dMVM -help contains an example for a main effect of group.
Thank you again!
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tamtam
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AFNI Message Board
Hello,
I have a question about running 3dMVM. I would like to run a 3 Group x 2 Phase x 2 Reinforcement repeated measures ANOVA and I am not sure whether I should specify "glt" or "glf" -what is the difference between the two? Are "glf" only for variables that have more than 2 factors?
I have provided my code and a breakdown of my ANOVA below.
Thank you,
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tamtam
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AFNI Message Board
Thank you very much for reviewing the values.
Yes, I used a blur of 4 via the afni_proc.py. Based on my protocol, my voxels for my epi volumes are 2x2x3mm and for my anat volumes are 1x1x1.
For the mask, I came across a few threads indicating the use of 3dmask_tool. I created and ran the following code below on a few participants and this seemed to work well. Is there a reason that the gro
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tamtam
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AFNI Message Board
Hello AFNI experts,
I am using Clustsim for the first time and I would like to make sure I am using it correctly. I have also read several posts on the message board and the AFNI –help files but I have a few questions.
My current steps:
(1) Run the 3dFWHMx code on each participant
3dFWHMx -input errts.Proc_9790_April2019+tlrc.HEAD -mask mask_group+tlrc.HEAD -acf
(2)Take the average o
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tamtam
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AFNI Message Board
Hello,
I have a question regarding the necessity of running 3dwarp -deoblique. I have ran my data through @SSwarper to perform non-linear registration, and I am currently running my pre-processing script I created using the uber_subject.py. I continuously see warning messages regarding my data's obliquity (see below). Is this something I should be concerned about? I have gone through the
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tamtam
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AFNI Message Board
Thank you very much for the suggestion. I re-ran my pre-processing after adding "real" timing values. Below are the 3dDeconve.err outputs before and after I added these timing values. I think they look okay. Do you think so too?
Thank you very much!!
BEFORE REAL TIMING VALUES ADDED (These just included -1:1 * per run)
*+ WARNING: '-stim_times_AM1 19' didn't read
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tamtam
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AFNI Message Board
Hello,
I created regressors to model when participants made a (1) correct response (2) incorrect response (3) did not respond at all. My regressors are structured as such: (stimulus onset): (duration).
I have time points for the "correct responses" and "incorrect responses" regressors, but sometimes I don't have any time points for the "did not respond at all&q
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tamtam
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AFNI Message Board
Hello,
I was wondering whether there is an objective value and threshold I can use to omit participants from group-level analysis based on the amount of movement they made during the task?
My data set contains a healthy control group and a group of patients that are prone to extensive movement. I have pre-processed my data and completed the quality check using the SS_review_driver command
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tamtam
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AFNI Message Board
Hello,
I was wondering whether there is an objective value and threshold I can use to omit participants from group-level analysis based on the amount of movement they made during the task?
My data set contains a healthy control group and a group of patients that are prone to extensive movement. I have pre-processed my data and completed the quality check using the SS_review_driver command.
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tamtam
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AFNI Message Board
Hello,
I ran 3dMVM and for one of my results, the activation spans across several areas of the PFC as a single cluster. We want to separate this cluster by the anatomical regions. In my lab, we have previously created a mask using existing AFNI ROIs (e.g. in the AFNI GUI selecting Define DataMode PluginDraw dataset…etc); however, I am not sure whether this would be appropriate as the atlas I
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tamtam
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AFNI Message Board
Thank you very much for the clarification! I ran my code successfully and it seemed to work.
I was reviewing the 3dMVM post and I saw that for the gltCoding it indicated:
"...for example, the following 'Group : 1*A -1*B & 1*A -1*C' tests the main effect across the 3 groups A, B, and C. Important Note: this option is only valid for
a hypothesis that involves bet
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tamtam
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AFNI Message Board
Hello,
I am attempting to set up a code to utilize 3dMVM and I have a few questions below regarding this set up. I would like to complete a Group (2) x Phase (2) x Reinforcement (2) x Subjects (38) ANOVA, and I have an unequal number of participants within each group. Before, I tried to use GroupAna, but realized I could not run this program as I have too many factors and had an unbalanced des
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tamtam
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AFNI Message Board
Thank you Gang for the suggestion. I am just looking into 3dMVM right now for the first time and I am going through the examples. If is still suggested that I include subject as a random effects if I use 3dMVM?
Thank you,
Tamara
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tamtam
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AFNI Message Board
I was hoping to run a 4-way ANOVA:
Group (2) x Phase (2) x Reinforcement (2) x Subject (38)
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tamtam
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AFNI Message Board
Hello,
I am hoping to start some group analysis and I have downloaded the AFNI Matlab Library from this website:
I just want to confirm that this is the latest library I should be downloading for analysis.
Than you in advance for your help.
Best,
Tamara
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tamtam
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AFNI Message Board
Great, thank you! I updated the AFNI binaries and used the updated script (pasted below). Out of curiosity, how long does the script take to run? I have been processing this script for nearly 18 hours....
Thank you,
Tamara
Code
@SSwarper \
-input 11987.anat+orig \
-base MNI152_2009_template_SSW.nii.gz \
-subid 11987
Terminal output:
-------- freesurfer-Linux-centos6_x86_64-stab
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tamtam
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AFNI Message Board
Hello AFNI,
I was hoping to get some clarification on the appropriate @SSwarper code I should be using.
I have been using the following code to run the @SSwarper:
@SSwarper \
11987.anat+orig \
MNI152_2009_template.nii.g \
11987
However, upon corresponding with an AFNI gurus, I realized that I was running the old @SSwarper and that I could run the following
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tamtam
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AFNI Message Board
That worked! Thank you so much!! I assume that since I have the old @SSwarper, I am utilizing the MNI152_2009_template.nii.gz which has 1 volume instead of the MNI152_2009_template_SSW.nii.gz which has several?
Interestingly, I did try using the "old" syntax and @SSwarper wouldn't run. It seemed to be taking an awfully long time and produced several "junk" files. I hav
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tamtam
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AFNI Message Board
Thank you for the clarification! I will subscript to the email list so I am up to date with AFNI software.
When I run afni -ver I get the following output:
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
My afni_proc.py script is:
# script generated by the command:
#
# afni_proc.py -subj_id SSwarp_proc_9409_aug30 -script SSwarp_proc_9409_aug30
by
tamtam
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AFNI Message Board
Thank you for your reply. I think it has to do with my @SSwarper script possibly?
I downloaded the MNI152_2009_template_SSW.nii.gz template and put it into the subjects folder. This is where I am running my @SSwarper code.
This is the current code I am using for @SSwarper.
@SSwarper \
9409.anat+orig \
MNI152_2009_template_SSW.nii.gz \
9409
Thank
by
tamtam
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AFNI Message Board
Below is my full script. I tried to re-order my blocks by putting the volreg blocks prior to the tlrc_NL blocks but I am still receiving the same error message
Script:
afni_proc.py -subj_id SSwarp_proc_9409 -script SSwarp_proc_9409 \
-scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat /home/bmiadmin/Tamara/PRR_Analysis/9409/9409.anat+orig
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tamtam
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AFNI Message Board
Page 2 of 3
Pages: 123