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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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Results 1 - 30 of 39
Hi paul,
This is a reasonable hypothesis from my observation.
If the voxel order was in "RAI" according to 3dinfo, the "voxel_order" field in the header stored in the .trk output should be "LPS".
I had not try the order of "IPL".
And I am not sure whether it will affect the coordinates stored in .trk data.
If not, I think simply fixed the "vo
by
lzhyoung
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AFNI Message Board
Hi Paul,
I am sorry for raising this topic again. I know you might not be interested in the old trk.
However, I can not abandon it for some historical reasons in the laboratory :(
I had met a difficulty in opening .trk data from 3dTrackID using matlab. The problem was solved by simply run "spline_filter", another command in the diffusion toolkit, on the trk output from 3dTrac
by
lzhyoung
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AFNI Message Board
Hi Paul,
Thanks very much!
Besides of the "vox_to_ras" field, the "n_count" field is also wrong.
I guess that the trk from 3dTrackID might specified wrong information in some field or just because some field were missed and made all in wrong order.
If possible, I suggest producing a correct header file for trk output.
If not, we have to turn to other suite that can produ
by
lzhyoung
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AFNI Message Board
Dear Paul,
I pre-processed my DTI data using afni and fatcat and output a trk data.
I met a problem to read in the trk data.
It seems that the "vox_to_ras" field is 0 in the trk output by 3dtrackID, which means "the matrix is not recorded" (http://www.trackvis.org/docs/?subsect=fileformat).
I would appreciate it if you can kindly check whether you had set the field correct
by
lzhyoung
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AFNI Message Board
Using the brainnetome altas, the mask in MNI space can be automatically labeled.
You can download it here:
Then
@AfniEnv -set AFNI_SUPP_ATLAS_DIR path_of_your/brainnetomealtas/brainnetome_dist
-lz
by
lzhyoung
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AFNI Message Board
Hi all,
I found that it is returns nothing if I using the command "whereami" to get anatomical label if my dataset is in MNI space.
The "Where am I" in the right-click recipe works very well.
However, I want to get a summary of the proportion of the overlap of the whole cluster with the brain atlas, not a single coordinate.
Thanks very much!
-Lz
The below is an
by
lzhyoung
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AFNI Message Board
Hi Rick,
Thanks for your reply!
I have no idea to fix this problem since I posted this question.
This is the output using your command.
(BTW, I use ubuntu 16.04 subsystem within windows 10.)
lzyang@~$ tcsh -c 'echo $noclobber'
noclobber: Undefined variable.
lzyang@~$ bash -c 'echo $noclobber'
lzyang@~$
As you see, tcsh reported that this is an undefined variab
by
lzhyoung
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AFNI Message Board
Hi all,
I failed to use the -Clustsim option in an independent t-test on two samples (n1 = 22, n2 = 23).
My afni version:
Precompiled binary linux_ubuntu_16_64: Aug 22 2018 (Version AFNI_18.2.14)
my script:
datapath="../data"
3dttest++ -setA C2 \
s031 ${datapath}/stat_s031_MNI3mm_Blur6.nii.gz'[7]' \
s045 ${datapath}/stat_s045_MNI3mm_Blur6.nii.gz'[7]' \
s
by
lzhyoung
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AFNI Message Board
Hi Rick,
Thanks very much!
A recent paper (Di et al., 2017, human brain mapping 38:1723–1740) states that "imperfect decovolution may introduce spurious psychophysical interactions and how to avoid it".
I noticed that you are one of the authors of this paper.
I feel that the centering of psychological variable was mean to minimize the correlation between the main effect term and t
by
lzhyoung
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AFNI Message Board
Hi Rick,
Thanks very much for your reply!
I am doing some analysis on the classical false-belief localizer task. In the task, false belief question (10s) and the answer phase (4s), false photo question (10s) and the answer phase (4s) was separated by 12 seconds fixation. The order of false belief and false photo condition was randomized, of course.
In the initial analysis, I used a GAM to get
by
lzhyoung
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AFNI Message Board
Hi all,
I post this question for some statistical discussion on the nature of PPI (psychophysical interaction analysis).
During PPI analysis, the task regressor was also entered as a covariate to tease apart the connectivity originating co-activation during task.
The task regressor was modeled using hymodynamic functions such as GAMMA.
As the hymodynamic function can not fit our brain respo
by
lzhyoung
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AFNI Message Board
Dear afni experts,
In longitudinal studies, MRI and fMRI images of a subject at different time points were collected.
We can normalize the anatomical images independently as in cross-sectional studies.
However, this method neglect the within-subject information in spatial normalization.
There are longitudinal pipelines for morphology measures such as in freesurfer.
Do you think it is nec
by
lzhyoung
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AFNI Message Board
HI Paul,
Thanks very much for your help!
I think it can solve my problem.
-lizhuang
by
lzhyoung
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AFNI Message Board
Hi afni gurus (paul?),
It is said in the help page that the "-remove_inf_sli " option was only used for alignment but do not alter the final output.
I had played this option and found that the neck of the final output was cut.
Please kindly check whether the script is right.
my afni version is AFNI_18.0.25
best,
lz
by
lzhyoung
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AFNI Message Board
Dear AFNI gurus,
I am very happy to learn @SSwarper today, which I think is very useful to give us a clean brain.
I played this function immediately.
Interestingly, the anatSS file was not as good as the anatS file. Specially, the anatSS file was left with a slight border (residual skull) around the brain. The anatS file is perfect.
Although I think the anatQQ file is reasonably nice, it
by
lzhyoung
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AFNI Message Board
Dear AFNI experts,
I am facing a data set of brain tumor patients (T1, DTI and resting state data).
Do anyone have suggestions or experiences on normalizing those brain images with lesions using AFNI?
Thanks!
-lzy
by
lzhyoung
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AFNI Message Board
Hi all,
I am a little confused about the warning message "WARNING: Went over sparsity goal 718261 by 101, with a resolution of 0.000202".
The number in red was different among subjects.
Does it matter in group analysis because of different number of edges used to compute degreecentrality?
---------------------------- The script I used ----------------------------------------------
by
lzhyoung
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AFNI Message Board
Hi all,
I met the following errors when using 3dECM.
-lz
---------------------- THE ERROR MESSAGE ------------------------------------------
++ 3dECM: AFNI version=AFNI_17.2.17 (Oct 4 2017) [64-bit]
++ 11986 voxels in -mask dataset
++ vectim-izing input dataset
++ Detrending with polort = 1
++ Calculating ECM with FECM (sparsity=100.000%,thresh=-1.200,
scale=0.500, shift=1.000
by
lzhyoung
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AFNI Message Board
Dear all,
I met problems in using 3dSkullStrip to extract brain from some 3D structural images.
the right parietal and occipital lobe was missed after the Skullstrip.
I have tried methods mentioned in the help page of 3dSkullStrip.
It did not work.
You can download the file below for a check.
Thanks very much!
-Lizhuang
by
lzhyoung
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AFNI Message Board
Hi AFNI core group,
Thanks very much for your efforts in making the AFNI website great!
Everything is fine except that I can not find the change log of AFNI.
There was a link on the page of message board before the update.
I think it is very important for us to track what revisions have been made.
Please forgive me if I miss the link because of my carelessness.
-lz
by
lzhyoung
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AFNI Message Board
Hi AFNI experts,
I noticed that 3ddot output different values when the -demean option is on or off.
I guess that the output without -demean is not the person correlation.
the help documentation say the following:
-demean Means to remove the mean from each volume
prior to computing the correlation.
What is the meaning of the output value if I did not use the -demea
by
lzhyoung
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AFNI Message Board
Hi,
I use the new -clustsim option of 3dttest++ recently.
I always meet the error message below.
++ t-test randomsign:sh: 1: Syntax error: Bad fd number
sh: 1: Syntax error: Bad fd number
Although the error message is displayed, the 3dttest++ continues and finally with results.
Is this a potential problem need further care?
The output information for the -clustsim section:
by
lzhyoung
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AFNI Message Board
Hi Dr. Daniel,
Thanks very much for the Haskins Pediatric template and Atlas!
I am now using the Haskins template to normalize a set of anatomical images from children. However, I am a little confused about the label used by the Haskins Atlas. For example, the location [-54 15 11] (in LPI format) is labeled as ctx-lh-parsorbitalis 57. The name "parsorbitalis" is very strange for me.
by
lzhyoung
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AFNI Message Board
Hi afni Experts,
I always use afni_proc.py to process my fMRI data. I notice that extents masking is applied in the volreg step if I use tlrc_warp on functional dataset.
I read some people's script that do not use the afni_proc.py. Not all of them use extents masking.
So I wonder whether extents masking is a necessary step? What are the benefits of using extents making?
I read the
by
lzhyoung
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AFNI Message Board
Hi afni experts,
I compared the difference between 3dREMLfit vs. 3dDeconvolve.
At the individual subject level, more activations were found in 3dDeconvolve than 3dREMLfit.
At the group level, results based on the beta from the 3dREMLfit differed a lot from the analysis used the beta from the 3dDeconvolve.
So how can I choose which output is correct or suitable for group analysis?
BTW
by
lzhyoung
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AFNI Message Board
Hi Rick,
How to disable openmp on my MBP?
Will this setting affect other programs in afni?
Thanks very much!
lzh
by
lzhyoung
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AFNI Message Board
Hi Zhark,
I noticed that the afni has been compiled again on Aug 7.
Can I fixed the 3dQwarp problem by using @update.afni.binaries -d directly?
my current status is :
Version AFNI_2011_12_21_1014
[]
Thanks very much!
-Lzh
by
lzhyoung
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AFNI Message Board
hi,
I need to clarify the problem. Actually, it seems that the 3dQwarp had been freezed instead of running for several hours.
by the way, my MBP use snow leopard 10.6.8.
I noticed that there were posts on similar problems.
It was said that the "macosx_10.5_Intel_64icc.tgz" can help this problem.
However, I can not download the file.
Is there are some new advancement in resolving
by
lzhyoung
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AFNI Message Board
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