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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
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thank you for you valuable information. i attached the "vstat" section. how can we comment this incident?
by
osman
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AFNI Message Board
Hello there:
i am tring to do the resting-state fmri analysis. i did the preprocessing step using afni_proc.py then i did the first level analysis to detect the DMN network but when i underlay the resulted anatomic dataset and overlay the resulted the correlation maps i get a correlatin outside the brain borders(The areas outlined in blue).
Here is the afni proc py used in the preprocessing:
by
osman
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AFNI Message Board
thank you rick
i rewrite the command like this:
set dirA = /home/osman/Deneyler
set mask_dset = /home/osman/Deneyler/s01/s01.results/pACC.z+tlrc
gen_group_command.py \
-command 3dttest++ \
-write_script cmd_ttest.tcsh \
-prefix out_ttest \
-dsets $dirA/s*/s*.re
by
osman
-
AFNI Message Board
i get this output when i run the tcsh -x cmd_ttest.tcsh command:
osman@osman-VirtualBox:~/Deneyler/s01/s01.results$ tcsh -x cmd_ttest.tcsh
set data_dir = /s01/s01.results
3dttest++ -prefix out_ttest -setA setA pACC.z+tlrc.HEAD /s01/s01.results/pACC.z+tlrc*HEAD[0] -mask
++ 3dttest++: AFNI version=AFNI_22.1.04 (Apr 18 2022) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as L
by
osman
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AFNI Message Board
this is the command used to execute that 3dttest++ script:
set dirA = /home/osman/Deneyler
set mask_dset = /home/osman/Deneyler/s01/s01.results/pACC.z+tlrc
gen_group_command.py \
-command 3dttest++ \
-write_script cmd_ttest.tcsh \
-prefix out_ttest \
-dsets $di
by
osman
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AFNI Message Board
Hi rick-
i am using Ubuntu 20.04 and i converted it frombash to tcsh but still get the same resulted script.
here is the command used to execute the cmd_ttest.tcsh script:
set dirA = /home/osman/Deneyler
set mask_dset = /home/osman/Deneyler/s01/s01.results/pACC.z+tlrc
gen_group_command.py \
-command 3dttest++ \
-write_sc
by
osman
-
AFNI Message Board
Hi ptaylor-
i am using Ubuntu 20.04 by the way.
here is the contenst of cmd_ttest.tcsh :
# apply any data directories with variables
set data_dir = /home/osman/Deneyler/s01/s01.results
3dttest++ \
-prefix out_ttest \
-setA setA \
pACC.z+tlrc.HEAD "
by
osman
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AFNI Message Board
thank you ptaylor:
after i make sure that the file pACC.z+tlrc in the right directory. i run the command you suggested above like this:
set dirA = /home/osman/Deneyler
set mask_dset = /home/osman/Deneyler/s01/s01.results/pACC.z+tlrc
gen_group_command.py \
-command 3dttest++ \
-write_script cmd_ttest.tcsh
by
osman
-
AFNI Message Board
Hello there;
i am tring to do the group analysis resting-state fmri using the 3dttest manually (because it can not import PyQt4.QtGui).
any way when i type the 3dttest commands to the Ubuntu terminal like this;
#!/bin/tcsh -xef
# created by uber_ttest.py: version 2.0 (December 28, 2017)
# creation date: Wed Feb 19 11:33:21 2020
# ---------------------- set process variables ------------
by
osman
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AFNI Message Board
Hello there;
what i am trying to say is it normal to see this signals outside of the brain in the error time series and what is this signals?
by
osman
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AFNI Message Board
can you sir explain what is the nature of this signals which seen in every where except the brain?
by
osman
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AFNI Message Board
Hi ptaylor;
actually i said correlation but i didn't mean it exactly . what i did so far is the preprocessing step using the afni_proc.py . then i underlayed the resulted anatomic data and overlayed the resulted fanaticor error time series and applied a thershhold value. so it is not a correlation it is kind of signal seen in every where except the brain. so i wonderd if i did the preproces
by
osman
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AFNI Message Board
Hi ptaylor. I add the option "-giant_move" to my afni_proc.py command and run the afni_proc.py command as you suggest above in the last replay. then i underlayed the final anatomic data and overlayed the error time series "errts.s01.fanaticor" like shown in the picture attached below. i applied a thershhold value to the error time series. is my preprocessing step is alright?
by
osman
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AFNI Message Board
i foun a folder in name of QC_FT.11b.rest in the subject results directory and after running the command above "afni_open -b QC_*/index.html &"
QC HTML web page was opend i printed this web page into a pdf file which including informations about the allignment and preprocessing stage but i did not understand what to do ; i sent the file by the e-mail
my afni version is: Precompile
by
osman
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AFNI Message Board
Thank you ptylor
i did the preprocessing for one subject but when underlay the final anatomic data and overlay the error time series "errts.FT.11b.rest.fanaticor" i got a data match error as shown in the picture. so I can't go to the next step which is creating correlation maps.
by
osman
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AFNI Message Board
Hi i try to do resting-state fmri analysis for a 25 subject. when i run the example of afni_proc.py 11b i get this output:
osman@osman-VirtualBox:~/sub08224$ afni_proc.py \
> -subj_id FT.11b.rest \
> -blocks despike tshift align tlrc volreg blur mask scale \
> regress
by
osman
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AFNI Message Board
sorry but still do not know how can i creat the shell script As shown in the attached picture.
thank you
by
osman
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AFNI Message Board
how can i creat the shell script in order to do the preprocessing step for all subjects of my resting-state analysis for 25 subject.
As shown in the attached picture.
than you
by
osman
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AFNI Message Board
thank you ptaylor for your useful information.
actually i want to do the resting-state fMRI analysis over mentioned data by seed-based correlation analysis.may i know what should i do first and what is the steps.
thank you so much..
by
osman
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AFNI Message Board
Hello
is there any tutorial or example to do resting-state fMRI analysis for 25 subject dataset. actually i do not know how to get start, there is many tutorials and documents over the internet which i did not understand.
dataset link ( NYU_TRT_session1 ):
by
osman
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AFNI Message Board
osman@DESKTOP-A849Q2J:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-19041-Microsoft
version: #1237-Microsoft Sat Sep 11 14:32:00 PST 2021
distribution: ubuntu 20.04 focal
number of CPUs: 8
apparent login shell: b
by
osman
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AFNI Message Board
is there any tutorial or example of resting-state fmri analysis.
i did not find a useful thing over the internet
by
osman
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AFNI Message Board
i installed the BiocManager and then the OmicCircos.
but i still get the same error:
The downloaded source packages are in
‘/tmp/RtmpBOscMN/downloaded_packages’
Installing: OmicCircos
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see
Execution halted
by
osman
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AFNI Message Board
Hi there;
i am using WSL Ubuntu 20.04 for resting-state fmri analysis.
when i type uber_subject.py command i get this output:
osman@DESKTOP-A849Q2J:~$ uber_subject.py
**** 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
and when i type apt-get install python-qt4 i get:
osman@DESKT
by
osman
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AFNI Message Board
hello there i need FATCAT for resting-state fmri analysis. i am using WSL Ubuntu 20.04
when i run command @afni_R_package_install -shiny -circos
i get this output:
osman@DESKTOP-A849Q2J:~$ @afni_R_package_install -shiny -circos
Installing: c('shiny','shinydashboard','plotly','colourpicker','data.table','gplots','RColorBrewer
by
osman
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AFNI Message Board
OK, is sent the output of:
Rscript -e "install.packages(c('Rcpp','brms'), dependencies = TRUE, INSTALL_opts = '--no-lock')" 2>&1 | tee o.rscript.txt
to your E-mail.
thank you ptaylor!
by
osman
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AFNI Message Board
thank you:
here is the output of the mentioned command grep -H ppa /etc/apt/sources.list.d/* /etc/apt/sources.list
osman@DESKTOP-A849Q2J:~$ grep -H ppa /etc/apt/sources.list.d/* /etc/apt/sources.list
/etc/apt/sources.list.d/c2d4u_team-ubuntu-c2d4u4_0_-focal.list:deb focal main
/etc/apt/sources.list.d/c2d4u_team-ubuntu-c2d4u4_0_-focal.list:# deb-src focal main
/etc/apt/sources.list.d/c2d4
by
osman
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AFNI Message Board
Hi there
I am trying to install AFNI for the first time on Windows 10: Windows Subsystem for Linux. i am using version of ubuntu of Ubuntu 20.04 LTS
i tried all the suggested solutions on the internet and the message board of afni but still when i run "afni_system_check.py -check_all" command get this output:
osman@DESKTOP-A849Q2J:~$ afni_system_check.py -check_all
---------------
by
osman
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AFNI Message Board