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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: 123
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Thank you, this solved the problem!
May I suggest adding this information to the error message and/or to afni_proc's help under -tlrc_NL_warped_dsets? Unless it is thought that this would lead to people making the mistake and "fixing" it by renaming the file instead of correcting the actual mistake.
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Pawel
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AFNI Message Board
Hello,
I wanted to ask if I understand the help correctly and not missing something.
In afni_proc.py I want to use a -volreg_base_dset that is different from -align_epi_ext_dset: MIN_OUTLIER vs. epi[0], the latter is otherwise removed by -tcat_remove_first_trs. As all epi volumes are aligned to MIN_OUTLIER, but epi[0] is used as a basis of anat alignment, any difference between epi[0] and
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Pawel
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AFNI Message Board
Hi all,
I am seeing what seems to a very weird problem with afni_proc.py. Maybe I am making a mistake which I fail to see, but I can't really see one.
I should also say that I have a good workaround, so if no one wants to look at this, it's fine. I am just curious what's going on, and if there is my mistake I would like to learn about it. In the future there may be no worka
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Pawel
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AFNI Message Board
Hi Paul,
this seems like another great option, thank you. The good thing is that I don't even need to run adjunct_aw_tableize_roi_info.py, I have these 1D files from animal_warper being run on an earlier stage. Probably the 1D files are easier to re-format than the output of 3dROIstats, but then the latter is guaranteed(?) to stay there. I'll use one if these methods.
Pawel
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Pawel
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AFNI Message Board
The purpose is to use the labels externally in my Matlab scripts, this is why I want them in an external file, and why I want only keys and labels that were actually used by the atlas.
The original CHARM/ARM/SARM atlases come with text files listing keys and labels for each level, e.g. ARM_key_6.txt. I want to have something equivalent for my reduced atlas.
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Pawel
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AFNI Message Board
Apologies for talking to myself so much, but I think I almost got there
set nvi = `3dinfo -nvi ${IntBrainUARM}`
foreach atlas_level ( `seq 0 1 ${nvi}` )
3dROIstats -mask "${IntBrainUARM}+tlrc[${atlas_level}]" \
-nomeanout -key \
"${IntBrainUARM}+tlrc[${atlas_level}]" \
> ${IntBrainUARM}_${atlas_level}_ROIs.txt
end
The format of the result
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Pawel
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AFNI Message Board
I think I should explain it better.
I am creating an atlas is a subset of the ARM atlas. ROIs that do not belong to the frontal lobe, temporal lobe, telecephalon, or diencephalon are removed. A mask covering these regions is created from subbrick 0, and the applied to all subbricks.
This done as follows (note - lateralization is removed earlier, corresponding L & R ROIs have the same c
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Pawel
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AFNI Message Board
Thank you, this is very helpful.
Is there also method to extract such unique integer voxel values for a dataset that has no atlas point nor data table?
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Pawel
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AFNI Message Board
This is probably a very simple thing, but I can't figure it out.
If I have a 3d data file with integer values only, how can I obtain a list of unique voxel values in the file or in a subbrick? For example, doing this to the standard segmentation produced by @animal_warper should output something like
0
1
2
3
4
If there was a way to extract any labels associated with the ROIs, tha
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Pawel
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AFNI Message Board
xy497 Wrote:
-------------------------------------------------------
> 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
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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
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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
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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.
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Pawel
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AFNI Message Board
Oh I see. I had the template versions unpacked to separate subdirectories.
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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?
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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
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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
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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
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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
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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
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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.
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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
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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
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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
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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!
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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
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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
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Pawel
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AFNI Message Board
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Pages: 123