Show all posts by user
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
Page 3 of 4
Pages: 1234
Results 61 - 90 of 94
The size of input is ~1.2G resting data with 1200 volumes.
The output can be in 2.png.
by
charujing123
-
AFNI Message Board
Hi AFNI experts.
I have run the afni_proc.py, then it created the proc.sub. Then I try to run this by tcsh -xef proc.sub. However, it echo this message (see 1.png) below after several steps.
my afni is AFNI_17.3.01, under CENTOS 5.11 final system (x64). And, the sever has ~40G memory.
Thanks.
by
charujing123
-
AFNI Message Board
I have performed the resting state analysis. this is my script:
====
afni_proc.py -subj_id CON_EIU24 \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat CON_EIU24_SurfVol.nii \
-anat_follower_ROI aaseg anat aparc.a2009s+aseg.nii \
by
charujing123
-
AFNI Message Board
Hi Glen
If activation was in MNI space, can i use MNI_N27_both.spec and MNIa_caez_N27+tlrc to map the activation onto surface? If so, can i use MNIa_caez_ml_18+tlrc to create surcortical area, then I can map striatum onto surfaces?
Thanks.
Best.
by
charujing123
-
AFNI Message Board
Hi Glen,
Thanks.
It's working. It didnot change the surface, when I press "." or ",". Why? suma -onestate -i *Caudate*gii *Putamen*.gii *Pallidum*.gii -sv TT_N27+tlrc
Best.
by
charujing123
-
AFNI Message Board
Hi Glen,
Thanks.
Can you send me an example of atlas for the striatum? Then, i can try to map the region onto the surface. Or, it there any spec file that contain striatum segment?
Best
Rujing
by
charujing123
-
AFNI Message Board
Hi Glen
Thanks. Another question is whether the program represent striatum onto surface automatically?
Best.
Rujing
by
charujing123
-
AFNI Message Board
Hi AFNI experts
I want to show my activation results using surface based representation, just as attached file.
I downloaded suma_TT_N27, unfortunately, I donot know how to do next. Activation map was Talairach coordinates. AND, how to represent subcortical regions, such as striatum?
Thanks.
by
charujing123
-
AFNI Message Board
Hi afni experts,
I want to perform SVM at resting state data to train and predict individual behavioral index. However, the 3dsvm seems working at task state fmri data only. How can i perform it at rest-data.
Thanks.
rujing
by
charujing123
-
AFNI Message Board
3dTrackID -h_view
** ERROR: No GUI editor defined, and guessing game failed.
Set AFNI_GUI_EDITOR in your .afnirc for this option to work.
AFNI was run at windows 10 ubuntu subsystem.
rujing
by
charujing123
-
AFNI Message Board
Hi Pt
Year. I have run all the steps in the afni installation in WIN10. For the afni_system_check.py step, it did echo one error to fix; and I post this message in anoter topic.
I have tried some program for fun. I met one trouble until now: Open the AFNI, see TT_N27+tlrc, right click the image, select the "where am i". In principle, it should echo the coordinates, brain region name
by
charujing123
-
AFNI Message Board
Hi
I see. Thanks.
Another question: The command displayed some message after running afni_system_check.py -check_all. How can I fix it?
=========
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.24 (amd64)
have Ubuntu system: Ubuntu 16.04 xenial
have Ubuntu afni : Precompiled binary linux_
by
charujing123
-
AFNI Message Board
Hi all
As bad download speed in our lab, I did not know whether this step was done appropriately (windows 10 subsystem ubuntu 16.04). So I prefer install packages one by one manually. Can anyone tell me which packages( and version) in R (version 3.4.3) were needed for AFNI program?
Thanks
Rujing
by
charujing123
-
AFNI Message Board
hi,
I tried istall afni in windows via . however, I met a problem:
======
suma -update_env
suma: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
===============
how to fix it?
by
charujing123
-
AFNI Message Board
Hi AFNI experts and users.
Is there any template for mice? Such as cerebellum.
Thanks.
by
charujing123
-
AFNI Message Board
Hi all
I have many MNI coordinates. I know the whereami can report MNI to tlrc. However, I wonder how to get many tlrc coordinates by one script.
Thanks.
Rujing
by
charujing123
-
AFNI Message Board
Hi Cox,
This was the progress report in the console:
./mvpa_a7_ddt_newttest
Mon Nov 20 23:10:31 CST 2017
mkdir: cannot create directory `ttest_result': File exists
SB IS /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_10+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_11+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_12+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_13+tlr
by
charujing123
-
AFNI Message Board
Hi Cox
Sorry, I did not mean that. I just didnot understand the description of permutation test in 3dttest++. Why running 1000 of t-tests not running 1000 of means?
Thanks.
by
charujing123
-
AFNI Message Board
Hi rick. Thanks for your help. It crashed too fast to see the memory load. But it echoed information memory usage chunks =8131 Bytes=1520157 when i set the etac only 1. By the way, the memory in computer is 64G.
by
charujing123
-
AFNI Message Board
It echos errors when I ran a 3dttest++. Here is an error report. Then I post a crash log.
Sat Nov 18 22:04:04 CST 2017
mkdir: cannot create directory `ttest_result': File exists
SB IS /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_10+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_11+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_accu_eq_12+tlrc /home/psylab15/sdl1/MVPA/accuracy/fmri_acc
by
charujing123
-
AFNI Message Board
Hi bob, i am interested in the permutation test in this option. In the document help, it said running 1000 of 3d ttest. My question is why 1000 of ttests, not 1000 of means.
Thanks.
Rujing
by
charujing123
-
AFNI Message Board
In 3dttest++, I found an option to calculate one-sample permutation test. The description was as follows:
===============
The new-ish options '-Clustsim' and '-ETAC' will use randomization and
permutation simulation to produce cluster-level threshold values that
can be used to control the false positive rate (FPR) globally. These
options are slow, since they will ru
by
charujing123
-
AFNI Message Board
Hi rick
thanks for your help. I have performed the scripts. I was surprised that the cluster size in 1-sided thresholding was bigger that those in 2-sided or bi-sided thresholding. To my knowledge, one sided test is less stringent that two sided test. So why the cluster size in 1-sided is the biggest?
Thanks.
by
charujing123
-
AFNI Message Board
the output of 3dFWHMx included four columns. I wonder which of three are a,b,c for -acf option in 3dClustsim.
Thanks.
by
charujing123
-
AFNI Message Board
I ran this command in ++ Compile date = Oct 26 2017 {AFNI_17.3.01:linux_xorg7}
3dClustSim -mask mask_temp+tlrc -NN 1 -fwhmxyz ${xx} ${yy} ${zz} -pthr 0.005 0.001 -athr 0.05 0.01 0.005 -iter 10000 -quiet -prefix all_sb_${var_name}_std_FWHM_alsim
Of course, this command was old. And it echo errors in this new version of AFNI. The errors were:
========================================
++ Numb
by
charujing123
-
AFNI Message Board
Page 3 of 4
Pages: 1234