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History of AFNI updates
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xy497 Wrote:
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> Brilliant！
> I must log in to thank you for your solution!
> I'm in the same situation: Win10, WSL1, Ubuntu18,
> and get stuck at libnode64.
> This works for me!
Happy to hear that.
By the way, after months of struggle with WSL1 I gave up. It was especially bad at my institution - our IT securi
by
Pawel
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AFNI Message Board
Hi Clem,
sorry for jumping into your thread, but I am a fellow AFNI/NHP/MION user who has been struggling with similar issues.
So you did you get it to work with 3dSkullStrip and -skullstrip_opts -monkey and cost lpa+ZZ, correct?
For me, both 3dSkullstrip and 3dAutomask always failed on a subset of session (each in its own distinct way), but I found out that no epi skullstripping and l
by
Pawel
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AFNI Message Board
Hello,
I have a simple monkey/animal_warper/afni_proc.py question. I am modifying the MACAQUE_DEMO_REST pipeline.
If I want to use eroded WM signal as a nuisance regressor in afni_proc (whether via anaticor or as averaged WM), and I have WM mask from the NMT template, I should import the mask in NMT space into afni_proc, correct?
So this:
afni_proc.py
by
Pawel
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AFNI Message Board
Hi all,
I have been trying to do anaticor on NHP data. I think I realized I have been doing it in a stupid way, but now I have an idea how to do it more sensibly. I still have a lingering feeling that I my thinking might be wrong, so I though I'd ask here. First, am I right that the first idea was not good? Second, is the new idea OK?
Here are the details
1. Old (stupid?) idea.
by
Pawel
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AFNI Message Board
Oh I see. I had the template versions unpacked to separate subdirectories.
by
Pawel
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AFNI Message Board
NMT2 has several versions, I am using the 05mm version.
So for the environment variables, I should use
~/REF_TEMPLATES/NMT_v2.0_sym_05mm
not
~/REF_TEMPLATES
correct?
by
Pawel
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AFNI Message Board
Thank you. This is how I have been basically working, with the exception that we are still scanning subjects for the project. I have been happy with AW results in all monkeys (they all have their anat scans done), and with AP results from one monkey. Once I started expanding to another monkey (we have full functional datasets from 2, just starting another 2), things started going sideways, epi-a
by
Pawel
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AFNI Message Board
Hi Paul,
thank you, this makes me rethink my workflow. I am also concerned whether this issue might affect the analysis itself - I'll get to it at the end.
Let me describe the workflow quickly - you may or may not remember it from the previous conversations, but I also want to make it clear in case anyone else reads it and learns from it.
So the pipeline is based on MACAQUE_REST_D
by
Pawel
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AFNI Message Board
Thank you, looking there was pretty revealing.
Under "template": I had the correct file but the path was for HPC, not for my local computer, on which I ran the analysis.
Normally my scripts are safe against running part of the analysis in one context and another part in the other, but earlier today I was experimenting with something and apparently somehow got these folders crosse
by
Pawel
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AFNI Message Board
I ran afni_proc.py-based analysis and it produced no QC folder. I may have done something wrong in setting up the analysis , but I can't figure out what. I would appreciate suggestions...
Here is the relevant part of the output:
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
++ Found 40 files for QCing.
Traceback (most recent call last):
F
by
Pawel
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AFNI Message Board
Kyrie, you may have eliminated these possibilities already, but various minor departures from the expected syntax of the set command may produce this error. I do not see such departures in the script you posted here, but clearly it was edited for posting (you don't actually have a directory called 'abunchofdirectories', right?).
Things that would produce such error are missing
by
Pawel
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AFNI Message Board
Thanks!
The solution I used in the meantime was far less elegant:
-expr 'a + (b + 1000*bool(b)) * not(equals(bool(a)+bool(b), 2))'
maybe because I built on my original
-expr 'a + b + 1000*bool(b))
(which assumed no overlap) and I did not think of streamlining.
By the way, avoiding overlap does not fix the problem with the longnames messing up the label table.
by
Pawel
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AFNI Message Board
Hi Paul,
I've been in touch with Adam. Yes there is overlap, I found it in the meantime. I misread an earlier email from Adam. It will add handling that overlap to my code. I agree that for proper analysis I need to wait until Adam does it properly, this is just to have a quick look at the data.
Curious thing about long names, as this feature is documented in @Atlasize help. I am wonde
by
Pawel
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AFNI Message Board
Update: making a 2-column key file and using:
@Atlasize -dset ${FARMfile}+tlrc \
-lab_file ${FARMkey_file} 1 0 \
-atlas_name FARM
makes it work fine even if without long names. If am still curious how to add long names correctly, but it's less of s pressing issue now
by
Pawel
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AFNI Message Board
Hello everyone,
while waiting until official combined macaque SARM+CHARM atlas is produced, I tried to make an ad-hoc combined version ("FARM") to be able to have a first look at my resting state data.
I put together CHARM + SARM while adding 1000 to SARM keys. I was ensured that there was no spatial overlap between SARM & CHARM, so I did not check for that. I made a new key
by
Pawel
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AFNI Message Board
Thanks, Paul!
I think it must have been pretty subtle given that a dataset from the same monkey, just a different session, did go through. I am glad I could (indirectly) contribute to AFNI becoming a tiny bit better!
by
Pawel
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AFNI Message Board
Hi Paul,
sorry I think after several hours of testing I failed to convey my points in my lengthy post. Let me try again, briefly:
1. I only have a problem with skullstripping, I mentioned TNSR and gen_... just to say I see differences but I think not relevant.
2. I think I can provide a data/script combo that fails on 21.0.13 and works fine 20.3.03. Though I noticed the change between 2
by
Pawel
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AFNI Message Board
The script I am working on began to fail, and the failure point seems to be in 3dSkullStrip run by align_epi_anat.py run by afni_proc.py run by a heavily modified derivative of MACAQUE_DEMO_REST
It occurs with a specific data set (session 1). Another very similar data set (same experiment, same subject, different session (3)) runs fine. But the problematic session 1 was analyzed in the same w
by
Pawel
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AFNI Message Board
afni -ver
Precompiled binary linux_ubuntu_16_64: Mar 3 2021 (Version AFNI_21.0.13 'Titus')
@animal_warper -ver
3.31
For what I am working on now I am fine without copying my followers. I have them listed in a variable and instead of making copies (multiple, because one per subject) I can just use the follower I need via $refseg[1]. (I am modifying MACAQUE_DEMO_REST for my purpo
by
Pawel
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AFNI Message Board
Should @animal_warper copy atlas and segmentation followers to the output directory? Help suggests that it should (see below), but I do not see anything like that in the output directory. What am I missing here?
Main datasets ~2~
The following are all contained in the main output directory
("-outdir ..")
[..]
+ Template dsets and followers in template space
by
Pawel
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AFNI Message Board
Thank you, this generated correct proc script. Now running it, fingers crossed!
by
Pawel
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AFNI Message Board
Hello,
I am modifying MACAQUE_DEMO_REST to work with my data. Experimenting with EPI-anat alignment, I found that EPI stripping with 3dAutomask fails with my data but stripping with 3dSkullStrip works fine.
So in my modified script I start afni_proc.py with the following options:
set cost_a2e = "lpa+ZZ"
[...]
afni_proc.py
by
Pawel
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AFNI Message Board
Thank you. I am sticking to WSL 1 for two reasons: first, as you said, CIT keeps us on a version of Windows that does not run WSL 2. Second, it seems that getting AFNI GUI to work on WSL 2 is over complicated... I tried it on a non-gov machine with WSL 2, ran into problems, got some suggestions from you (https://afni.nimh.nih.gov/afni/community/board/read.php?1,159772,165003#msg-165003) but they
by
Pawel
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AFNI Message Board
Whatever the name will be, is there a plan when the name would be available?
by
Pawel
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AFNI Message Board
"being integrated a bit with another project (SARM)"
Does this mean that they will be combined into FARM (Full hierarchical Atlas of the Rhesus Monkey brain) at some point? That could be useful!
by
Pawel
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AFNI Message Board
Hello,
this is not really an AFNI question but it is related to using AFNI so I hope it's still OK to post.
I am encountering a weird problem while using AFNI on an NIH-owned Windows laptop, working from home.
AFNI is installed on Ubuntu 18.04 which runs on WSL 1.
As an NIH employee, every now and then I have to VPN to NIH network to do various things that are not accessible fro
by
Pawel
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AFNI Message Board
Hi everyone,
I recently went 3 times through installing AFNI on Ubuntu 18.04 on WSL1 on Windows 10, and each time I run into a problem with installing brms, which was not solved by the suggested solution, i.e.:
sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
sudo apt update
sudo apt install -y r-cran-rstan r-
by
Pawel
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AFNI Message Board
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