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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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Hi, I have exactly the same problem. Any update on that?
Thank you
Simone
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Simone Cauzzo
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AFNI Message Board
Yes, thank you very much for the script. I wanted to reply to you when I had some news or questions, but unfortunately this is a side project on which I don't work full time, and I still have some tests to do. I will update you probably next week.
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Simone Cauzzo
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AFNI Message Board
PS: now I have all the tools, but of course a scriptable way to insert markers in the header would be awesome.
Is there any news on the plug_tag.c function? Or maybe some way to use the tagset.h file?
EDIT: I SEE THAT ACTUALLY 3DTAGALIGN HAS A -TAGSET OPTION THAT ALLOWS TO USE .TAG FILES WITHOUT HAVING TO INSERT TAGS INTO THE HEADER. SO I GUESS I FIGURED OUT HOW TO SOLVE THE LAST ISSUE AS WEL
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Simone Cauzzo
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AFNI Message Board
Wow, 3dNwarpXYZ is exactly what I was looking for, thank you, I couldn't find it. I'll work on it, but yes of course, I would be happy to have that script!
Thank you for the excellent support
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Simone Cauzzo
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AFNI Message Board
Thank you so much for the detailed reply.
I managed to save the tags in the .HEAD using the plugin.
The 3dQwarp command I was testing is quite similar to the one you suggested, I only have to further test the workhard option. Using the option -iniwarp and always the same image as source I guess that I will have no problems of resampling.
Two more questions:
- I tested 3dTagalign: how is this
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Simone Cauzzo
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AFNI Message Board
Hi, thanks for the kind reply
I'm trying to coregister images acquired with confocal microscopy with 25 micron isotropic resolution to the NISSL coronal Allen brain atlas (https://mouse.brain-map.org/static/atlas) obtained by converting to nifti a stack of tiff. As I said, results are almost satisfying, in particular for what regards outer edges, while there is still space for improvement i
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Simone Cauzzo
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AFNI Message Board
Hi everybody
I'm working on 3d stacks of images of rat brains from confocal microscopy. I have to register them to an Allen standard template, so I'm testing AFNI on this.
I'm getting quite good results with 3dQwarp. Nonetheless, I need to further improve these results. I have a set of markers (or tagsets, as you call them in 3dTagalign) matching points in the atlas with points i
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Simone Cauzzo
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AFNI Message Board
Hi everybody
I have resting state data, TR=2.5s, 3 runs of 210 points per subject. The lab I'm working for had a pipeline making use of 3dFourier to perform bandpass filtering in the range 0.01-0.1 Hz, making it in two steps, fist highpass then lowpass.
I was trying to improve the code, I saw that 3dBandpass improves the demenaing of data, now I have a couple of questions
- what's th
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Simone Cauzzo
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AFNI Message Board
Hi Daniel, thank you very much for the useful suggestions. I came up with averaging after it gave me some improvements when I was still using fsl, but now I will pay more attention to subject-specific movement, thanks.
Also, I didn't know about epi_b0_correct.py, I'm glad it has been finally implemented
"I'm surprised you would get that much distortion between EPI and
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Simone Cauzzo
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AFNI Message Board
Hi Daniel, thank you so much for the reply, here are some more details
What I'm doing on 7T data (1.1mm iso) is:
1) applying motion correction and taking the bias-field-corrected time-average as base for registration (should increase SNR)
2) correcting for distortions using fieldmaps and fsl fugue
3) affine registration epi 2 anat with align_epi_anat.py
4) nonlinear registration epi 2
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Simone Cauzzo
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AFNI Message Board
Hi everybody
I'm trying to register functional data to the anatomical in 20 subjects in a study where both inferior medulla and cortex are involved in the analysis. I first tried the "usual" registration with align_epi_anat.py, the results on the cortex and superior brainstem were good, but I had some problems from the lowest part of the pons dawnwards. I used the suggested proced
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Simone Cauzzo
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AFNI Message Board
Good morning
I would like to perform an analysis with 3dREMLfit and 3dMEMA based on permutations. I mean, I would like to perform the estimation many times on surrogate data, in order to build the distribution of the statistic voxel by voxel.
Is there any advantage I can get from cluster computing? I have the possibility to work on clusters, but I'd like to know if this Is supported by AFN
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Simone Cauzzo
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AFNI Message Board
Good morning, I'm having troubles with 3dcalc. The line is
3dcalc -a 'mask_x+orig[0]' -b map_x+orig -expr 'b+step(a)*(a*(32+1)-b)' -prefix map_x_1
AFNI version is AFNI_18.3.03 (Oct 19 2018) [64-bit]. This line is inside a for loop, and it has been executed 30 times before giving the error. map_x is created by another 3dcalc line, and it is a 3D dataset, while mask_x i
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Simone Cauzzo
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AFNI Message Board
Hello everyone
I would like to use unWarpEPI.py to perform correction with opposite polarity data (blip-down). I was wondering why in the help of afni_proc.py it is recommended to use this program after tshift, and also where correction with retroicor should be placed in this context, whether before or after unwarping.
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Simone Cauzzo
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AFNI Message Board
It worked. Thank you so much, I'm sorry I realized I could fix it by my own, I just searched the wrong keywords
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Simone Cauzzo
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AFNI Message Board
I installed AFNI on my pc, following the instructions on the website, more than a year ago, and everything was going well. Today it was the first time that I tried 3dSkullStrip, so I don't know if the problem has always been present or if it new. Yesterday I installed ANTs, I don't know if this may have messed up something. Anyway, if I perform sudo apt-get install -y gsl-bin, it just s
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Simone Cauzzo
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AFNI Message Board
Good morning,
I'm receiving this error message when using 3dSkullStrip on Ubuntu 18.04.1 LTS 64 bit.
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
I've been working the whole day on this, and I saw that also other users reported the same problem, so I tried to follow previous posts in the community and to f
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Simone Cauzzo
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AFNI Message Board
Good morning,
I apologize for misunderstanding, I probably should have better explained my situation:
I am analyzing fMRI data with GLM and I'm trying to model neural activity related to CO2 levels during voluntary breath hold (repetitions of 30s free breathing and 30 s breath hold). The problem is that I have to test a huge number of models and decide which one is the best. Model selectio
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Simone Cauzzo
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AFNI Message Board
Good morning, I've done a subject-level analysis with 3dREMLfit using an amplitude-modulated stimulus. Then I used 3dMEMA to perform mixed-effects group analysis. I would like to correct for family-wise error using permutation tests instead of cluster-size based methods such as 3dClustSym. I've checked program randpermute.py (https://kurage.nimh.nih.gov/meglab/Meg/Randpermute) but for w
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Simone Cauzzo
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AFNI Message Board
Good morning, I was running 3dDeconvolve when I got this error
*** buffer overflow detected ***: 3dDeconvolve terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f57005d17e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f570067315c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7f5700671160]
/lib/x86_64-linux-gnu/libc.so.6(+0x1166c9)[0x7f570067
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Simone Cauzzo
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AFNI Message Board