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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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Thank you, I think I did @aw a shot early, it did not work out of the box, and I did not pursue. I might revisit. So far of Daniel's ideas I tried nmi but it did not go well with my data
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Pawel
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AFNI Message Board
Hi Daniel,
Thank you for the suggestions. Incidentally, earlier today I got a pretty good result with lpa on inverted T2 with some additional constraints. But I'll give nmi on non-inverted a try as well.
I did pretty tight box-cropping. I can try a sphere too, but my concern is that some of the scans were acquired with in front of the frontal poles and the occipital lobe was even parti
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Pawel
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AFNI Message Board
If you don't mind, I would rather prefer to share them directly with you via email, or an entire volume via OneDrive or Box.Is that OK?
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Pawel
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AFNI Message Board
Thank you, this seems like a great solution. Yes I verify L/R independently
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Pawel
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AFNI Message Board
Hi all,
I am working on some difficult NHP T2s that I need to align to NMT. They are difficult because some are not exactly complete (the rear and sometimes the very front of the brain is cut off), they have an implant artifact, and crucially in the most important area they have both a local change of tissue shape and a hypersignal. (my ultimate goal is to threshold that hypersignal or it
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Pawel
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AFNI Message Board
Hello good AFNI people!
I am converting NHP DICOM files to AFNI. These are anatomical T1 and T2 volumes from more than 1 scanner.
NHPs are oriented differently from humans in the scanner, they are scanned in the sphinx position, the scanner does not know that, so I need to fix the orientation while converting. I have been doing it using -orient_code in to3d, I figured out what code I need t
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Pawel
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AFNI Message Board
Actually, could it be made an environmental variable i.e. global setting at some point?
I thought I would be happy with
alias af 'afni -com "SET_XHAIR_GAP 1"'
and starting afni via "af"
But if then I open a new controller using the New button, it uses the default gap size of 5
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Pawel
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AFNI Message Board
Thank you, Paul. Actually, setting the gap size is more important for me, as I almost always want to switch it from the default 5 to a much smaller number, while only sometimes I feel like switching xhair color to yellow
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Pawel
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AFNI Message Board
Hi all,
Is there an environment variable to pre-set cross-hair color and gap size? I cannot find one on the variable list, only thickness and presence, but maybe I am missing something
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Pawel
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AFNI Message Board
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
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Pawel
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AFNI Message Board
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
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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
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Pawel
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AFNI Message Board
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
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Pawel
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AFNI Message Board
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
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Pawel
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AFNI Message Board
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
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Pawel
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AFNI Message Board
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
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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,
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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
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Pawel
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AFNI Message Board
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
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Pawel
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AFNI Message Board
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
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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
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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
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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.
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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
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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.
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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 \
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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
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Pawel
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AFNI Message Board
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Pages: 123