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In hindsight, I had a very good hint here:
++ 5519 voxels in ROI
++ 43959 voxels in atlas-resampled mask
I think I did not realize that ROI and mask refer to basically the same thing, and that the ratio of the two numbers is almost exactly 8, which strongly suggests resampling to twice the resolution.
I think I am going to register all three ARM atlases to my AFNI and, to avoid con
by
Pawel
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Hi Paul,
I think I know what happened.
I did not split the file, it had been split by ARM/NMT creators. The split versions are registered with AFNI as single-subbrick "ARM Level x" atlases, along with the full 6-subbrick "ARM". Probably to facilitate subbrick selection which - as we have found out - does not seem to work in standard way with whereami.
But here is the
by
Pawel
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AFNI Message Board
Daniel Glen Wrote:
-------------------------------------------------------
> This may have to do with differences in the
> resampling/interpolation to the template. Try
> resampling first with 3dresample to the grid of
> the template and nearest neighbor interpolation.
Hi Daniel,
resampling what to the grid of the template? I _think_ that all my files at this point are on
by
Pawel
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I know, but the ROI file I am using (Clust_mask_0001+tlrc) contains only one ROI, it was made by 'ing one specific cluster from GUI's clustering report.
Either way, if I use the ordered mask (-omask) mode on this single-ROI file, or ordered mask on a multi-ROI file, I get the same numbers on this ROI and regions: 41.8% and 32.3%, vs. 45.2% and 34.8% from doing it step by step or in
by
Pawel
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Per 3dinfo, both the atlas file and the ROI file are of the same geometry and orientation. Which is expected, as alignment happened on the way here, but I checked.
Both report:
Geometry String: "MATRIX(-0.5,0,0,31.75,0,-0.5,0,27.625,0,0,0.5,-7.875):128,156,100"
and
[-orient LPI]
But it really looks to me as if whereami was slightly off... I tried to replicate what (I thi
by
Pawel
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That does not work either for me:
whereami -atlas ARM"[3]" -bmask Clust_mask_0001+tlrc
++ Input coordinates orientation set by default rules to RAI
** ERROR: Atlas ARM[3] not found in list.
but again ARM seems to register each level separately in afni so
whereami -atlas 'ARM Level 3' -bmask Clust_mask_0001+tlrc
works fine.
I am now seeing some discrepancies betwee
by
Pawel
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I tried standard subbrick selector and it did not work
whereami -atlas ARM[3] -bmask Clust_mask_0001+tlrc -tab
++ Input coordinates orientation set by default rules to RAI
** ERROR: Atlas ARM[3] not found in list.
But this did!
whereami -atlas 'ARM Level 3' -bmask Clust_mask_0001+tlrc -tab
Sorry I did not figure it out myself
by
Pawel
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AFNI Message Board
Thank you!
I was able to get the first answer (what part of the ROI belongs to this and that atlas area) bu using whoami with -bmask or -omask, even if the output is not very machine readable.
Intersection of ROI (all non-zero values) with atlas ARM (sb3):
31.0 % overlap with CR_area_24, code 506
29.7 % overlap with CR_rostral_dlPFC
, code 559
12.1 % overlap with CR_area_8B,
by
Pawel
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AFNI Message Board
Hello all,
I have an (NHP) cluster map aligned to NMT, which I would like to cross check against the ARM atlas, to produce a report like:
cluster 1: 90% belongs to atlas area 75, 5% to atlas area 133, 5% to nowhere
cluster 2: 14% belongs to atlas area 22, 86 % to nowhere
and then
atlas area 55: 45% in cluster 1, 55% in cluster 3
atlas area 72: 12% in cluster 1, 88% in no cluster
not
by
Pawel
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Thank you. I did try messing with levels - though I think I asked it to start at 6 or 7, and to stop at a smallish patch. The idea was "do not touch the big picture, fix small differences". For some reason this was taking ages to calculate and I ultimately stopped it and re-ran from level 0 which ran considerably faster.
As for 3dNWarpCat - if this is supposed to work as I tried, I
by
Pawel
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Hi all,
I would be grateful for some more help...
As I said in the previous thread, my goal is to align an NHP T2 to the NMT template. Direct alignment does not work (in my hands) so I am using the same animal's T1 as an intermediate.
Step 1 is to align T1 to the template using @animal_warper and that works fine.
Step 2 is to align T2 and T1 and I am using align_epi_anat.py for t
by
Pawel
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AFNI Message Board
Hi Daniel,
thank you, adding:
-master_epi BASE
to align_epi_anat.py options solved the issue,
Just to see how it works I tried to go through 3dWarp too, but with no -gridset applied it cropped the T2 in the same way as in my original post.
However, providing the T1 as the gridset produced a virtually identical result to align_epi_anat.py with -master_epi BASE (minute diff
by
Pawel
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AFNI Message Board
Hi all,
as usual I feel dumb asking these questions because it feels as if I am missing something trivial... but I cannot figure it out myself.
I am using align_epi_anat.py to align an anatomical T2 to an earlier anatomical T1 in the same NHP. The overall goal is to align that T2 to NMT, but I wasn't able to do it directly. So I am using @animal_warper to align the T1 to NHP, and align
by
Pawel
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AFNI Message Board
Hi Rick,
just to clarify, I am using Oracle VM, not WSL - trying to run AFNI on Linux on WSL was far more cumbersome than via VM. But based on the information I have, the same problem may occur with WSL. Incidentally, the solution may be identical in both cases.
by
Pawel
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AFNI Message Board
Hi Rick,
I sent you an explanation by email, but I thought I would put it here as well, maybe it will be useful for someone in the future.
My Ubuntu runs in VM on Windows, and my script operates on folders that are shared with Windows. File operations on such folders are apparently handled by Windows (even if requested by Linux), and thus are case-insensitive. The script had wrong case in a
by
Pawel
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AFNI Message Board
Hi Daniel,
thank you for the explanation about different bases. These are 15-minute runs in a monkey, so I think that making an assumption of negligible movement between epi[0] and min_outlier, which may be anything from epi[2] to epi[409], may be too risky. I will probably revert to epi[0] for both.
I had thought that maybe something is going on with the file system, and I did try insertin
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Pawel
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AFNI Message Board
Thank you. For now I will probably use EPI[0] for both. I do not have a strong rationale for using separate bases, just wanted to see if it helps.
by
Pawel
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AFNI Message Board
By the way, I hope you don't mind if I quickly ask about a different thing,
This sequence:
3dAllineate -base $MPRAGE_file \
-input ${MDfile_u}+orig \
-prefix $MDfile_alMP_u \
-cost lpa \
by
Pawel
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AFNI Message Board
Oh, thank you for looking at this (and the other one) during weekend!
This is an NHP dataset which gives me a lot of trouble with EPI-anat alignment. Like I said in the other post, I am basically following MACAQUE_DEMO_REST so I am going to standard (NMT2.1) space, using animal_warper, now possibly adding another anat step, as described in the other post.
At some point, I spent a lot of ti
by
Pawel
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AFNI Message Board
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.
by
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
by
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
by
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
by
Pawel
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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.
by
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
by
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
by
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?
by
Pawel
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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
by
Pawel
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