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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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Pages: 12
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Hi,
Is it possible to visualize tracts in other formats with suma, such as trk from TractVis, or tck from MRtrix3?
If not, is it possible to convert trk/tck to .niml.tract?
many thanks!
Mengxing
by
Liu Mengxing
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AFNI Message Board
Hi,
I have one statistic question:
Say I have a within-subject repeated measure design, with two conditions A and V, I want to test if there are any regions more involved in A comparing to it in V.
Two approaches in my mind:
1) each condition has one regressor in the first level GLM matrix, resulting in beta for A and beta for V, for group level analysis, do paired t-test to test the dif
by
Liu Mengxing
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AFNI Message Board
oo yeah that's right, I missed that -I option. Now that makes sense to me!
Thanks rick!
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Liu Mengxing
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AFNI Message Board
Hi,
I have a afni_proc command to do the alignment from epi to anat:
afni_proc.py -subj_id sub03 -dsets dmeanf_sub03.nii -blocks align volreg -volreg_align_e2a -copy_anat T1.nii
the resulted proc.sub03 script has the align block codes like this:
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI reg
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Liu Mengxing
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AFNI Message Board
Hi Daniel,
In short, I'm using Ubuntu 19.04, and the afni version Precompiled binary linux_ubuntu_16_64: Mar 8 2019 : AFNI_19.0.24 'Tiberius'
Just in case you want all the details, I have it here.
Also, if it took you too much time, and there was no apparently stupid bug in my code, feel free to ignore my report. After all you won't have to save images often for one
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Liu Mengxing
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AFNI Message Board
Hi Daniel,
Even I tried with
DriveSuma -com viewer_cont -key "$pose"
sleep 3
DriveSuma -com viewer_cont -key 'Ctrl+r'
still didn't work.
And I tried it manually with GUI by myself, nothing went wrong.
What's weird is that sometimes the same codes worked perfectly, and sometimes it didn't.
Thanks!
Mengxing
by
Liu Mengxing
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AFNI Message Board
Hi afni group:
I have a DriveSuma script that runs afni and suma, has them talking and save images. It works perfectly on one machine. While when I moved it to another machine, everything went well except the recording behavior. Basically I use
for pose in 'Ctrl+left' 'Ctrl+right'
do
# get view and snap
DriveSuma -com viewer_cont -key "$pose" -com viewer_
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Liu Mengxing
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AFNI Message Board
Thanks Daniel for uploading the data.
I am trying to parcellate my individual subject brain with HCP parcellation, so I could extract the structure from each sub in native space.
I'm following the method below, except do it in each subject instead with MNI_152_T1.
— convert to nii
mri_convert ?h.Glasser2016.mgz ?h.Glasser2016.nii
— use Freesurfer to move from fsaverage to
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Liu Mengxing
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AFNI Message Board
Hi afni group,
Thanks for include the HCP atlas in afni/suma!!
I'm trying to extract the HCP parcellations from individual surface space, with the instruction of link here:
But I don't see how to get std.141.?h.HCP.annot.niml.dset from *h.HCPMMP1.annot. Maybe I missed something.
Anyway, I was doing functional connectivity in surface world, and I have extracted individual an
by
Liu Mengxing
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AFNI Message Board
Thanks for your reply! Got it worked!
While another bug of my code is that it does not save the image with the prefix that I defined with
export SUMA_AutoRecordPrefix="./${image_dir}/${image_pre}"
It still saved with the default prefix, which is /SUMA_Recordings/autorecord.jpg
Here is the full codes.
#!/bin/bash
#start a suma and wait it for 3 seconds
suma -spec std.141
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Liu Mengxing
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AFNI Message Board
Hi afni group,
I am showing data in surface world with suma_MNI152_2009.
What I usually do is to use the spec file std.141.MNI152_2009_lh.spec, and switch to the inflated surface.
command:
suma -spec std.141.MNI152_2009_lh.spec
When I tried to using DriveSuma to replicate what I did manaully,
with command :
DriveSuma -com show_surf -i std.141.lh.inflated.gii
It did show
by
Liu Mengxing
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AFNI Message Board
Dear afni,
I'm doing gPPI by following the pipline here:
In the cmd.ppi.2.make.regs part to make the regressors,there is one step generating the ideal IRF (starting from line 66) . There are two options in the demenstration, one using GAM and one BLOCK, with different durations.
My stimuli have varying durations, so when I do GLM, I used combination of -stim_times_AM1 and dmBLOCK.
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Liu Mengxing
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AFNI Message Board
Hi Rick,
The pipeline I adapted before I decided to move my analysis to surface world is using the combination of 3dclust, 3dclustsimand whereami to output the coordinates of peak activation and the label table scriptly.
But I don't see 3dclust could work on surface data.
What's the recommended way of output the activation peak coordinates and lable? If I could do this on surface
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Liu Mengxing
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AFNI Message Board
Hi Daniel,
Thanks for your reply!
If I define the voxel size as the functional data has, I guess I need one functional data as the grid_parent.
But my functional data are all in standard mesh surface world, and what I want to do is to leave the normalization as the last step to maximize the accuracy of correspondence across brains.
What I want to accomplish is, by doing surface to vo
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Liu Mengxing
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AFNI Message Board
Thanks Peter.
Tried also SurfVol as the grid parent, still got the unreasonable size of stats volume data (3.3G for each hemi). I could almost imagine how hard afni has to work to read it. Kind of feel sorry for my afni.
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Liu Mengxing
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AFNI Message Board
Thanks a lot Peter!
While, just to be clear, if I transform a surface data to a volume data with the suma_MNI152* spec and surfVol file, the resulted volume data will be in standard space(in this case, MNI space), right? There is no need to do any warp or @auto_tlrc?
Following the above question, I did the transformation with MNI152 spec and surfVol file, the volume data I got is super big,
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Liu Mengxing
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AFNI Message Board
Hi
Greetings!
I followed the surface-based analysis in afni_proc.py example 8, during which I mapped all participants volume to standard mesh surface.
Then I conducted the group analysis and got the group statistical results in surface world.
Q1: Trying to rendering the group statistical results in suma, I assume whichever participant standard spec file I use in suma does not matter
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Liu Mengxing
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AFNI Message Board
Hi Daniel,
Does suma have similar controlling option to change the font and button size? Couldn't find it.
Meng
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Liu Mengxing
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AFNI Message Board
Thank you both Gang and Daniel, I think I'll stick with the surface-based approach.
One tiny question: Does it make sense to mapping the group analysis results that are totally from volume world to surface rendering, just for showing the cortex contrasts?
Like, select the statistical results from method 1 as the overlay, and open suma, have the spec and sv as the group average, does it
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Liu Mengxing
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AFNI Message Board
Hi afni group:
I had two ways to do group analysis in my mind.
The first is based on the volume data, just simply @auto_tlrc the first level glts file for each participant and do anova (in my case, 3dMVM).
The second is based on the surface data. 1) do 3dVol2Surf on the first level glts file of each participant, 2) with the surface data (1d file) do the same anova, 3), do 3dSurf2Vol to t
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Liu Mengxing
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AFNI Message Board
Hi Rick,
Your suspicion is right, I updated to the latest version (previous version is AFNI_2011_12_21_1014), and the error was gone, everthing went well.
Thank you so much!
best,
Meng
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Liu Mengxing
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AFNI Message Board
Hi Rick,
Thank you for your recommend.
I tried make_stim_times.py as you suggested, then where was another problem.
As my runs have different TRs, I tried with the option -run_trs which allows me to define TR number for each run, as example 2b did in the command page.
But it gave me an error: missing option -nt
My command is
make_stim_times.py -files SW1D.mx -prefix stim_times_SW
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Liu Mengxing
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AFNI Message Board
Hi afni group,
I am using 3dDeconvolve to do subject level GLM, and I have the stim file as 0000011111000000000111, and also I have one from the afni function waver,
waver -TR 2 -numout 888 -peak 1.0 -input "$task"1D.mx > "$task"1D.1d
I wonder which one should I use when I define the parameter of -stim_file in 3dDeconvolve?
It's a block design with varying du
by
Liu Mengxing
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AFNI Message Board
Perfect, that will do by assigning the std to a variable and use it in 3dclust!!!
You work at weekends! Take a rest! although I am sooooo happy to have your reply without waiting for Monday.
best,
Mengxing
by
Liu Mengxing
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AFNI Message Board
Hi pt,
your reply is super helpful, while I still wander, if there is one way to threshold by specifying the q FDR value?
best,
Mengxing
by
Liu Mengxing
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AFNI Message Board
Hi afni group:
Greetings!
I wander if there is one way to threshold a statistical dataset by setting the q/p value, instead of using t/F value, by 3dclust/3dmerge, or you have other recommendation.
The reason I am looking for this method is that for different contrast, the statistical threshold could change with the same q value.
Many thanks!
Mengxing
by
Liu Mengxing
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AFNI Message Board
ok now i figured out it might be due to the graphic card driver in my local machine, when i switch to Intel GC, ssh to remote server and suma works fine!!!! While if I use Nvi card, it doesn't.
so now i will try to find a new driver for my Nvi graphic card.
Anyway, thanks for your time Daniel!!!
by
Liu Mengxing
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AFNI Message Board
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