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Dear AFNI users-
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Hi all,
I have been experimenting with non-linear alignment to see if I can improve my alignment issue. Below is an image of the best I could get with ginormous move (see first post)
I used 3dQwarp following the suggestion for aligning epi to T1 (though with a small modification to make it an anat2epi alignment, not epi2anat as in the example)
It has done a great job of aligning arou
by
hdempseyjones
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AFNI Message Board
Update (in case anyone is having the same problem)
SurfVols should have skull on by default. The one I was working with did not (I inherited it from a previous lab member and there is something not right with it)
I regenerated the surface model from the anatomical from scratch using recon-all in Freesurfer, then used suma make spec hires to generate the SurfVol again. SurfVol now is correct
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hdempseyjones
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AFNI Message Board
Update - this code works on my local computer, but does not run on my university's remote computer.
The IT person suggested it could be a problem with some of my environment variables.
Could someone suggest what environment variables I should check given the above error to try get DriveSuma working on my remote machine?
Or perhaps another thing to check/ try? Has anyone encountered
by
hdempseyjones
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AFNI Message Board
Hi there,
I am trying to learn how to drive suma from the command line by following the example from this video
I am using this code (running from inside the SUMA folder of my subject)
#!/bin/tcsh
## Set up vars
set subj = P007_FR
set spec_file = {$subj}_lh.spec
set surf_vol = {$subj}_SurfVol+orig
## Set up afni vars
set portnum = `afni -available_npb_quiet`
setenv SUMA_Driv
by
hdempseyjones
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AFNI Message Board
Hi sorry,
Images should be attached now. The one where alignment is better is using lpa, the warped one is lpa+ZZ
My questions were:
- My colleague said the lpa alignment was 'good enough' but is it?
- Why do I always get a weird warp when using +ZZ?
So, pt, you would recommend trying higher order alignment, e.g., non-linear methods as used in 3dQwarp or @SSwarper?
- Data q
by
hdempseyjones
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AFNI Message Board
Hi there,
I am trying to align my SurfVol to my experimental anatomy but I just can't get it to fit well enough. This is despite me nudging the SurfVol for a long time and getting it very close to the experimental anatomy.
The imaged I attached is as good as I can get (underlay: experimental anatomical (aligned to epi); overlay: SurfVol (aligned to experimental anatomy))
Background:
by
hdempseyjones
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AFNI Message Board
Hi Daniel,
Thank you for the suggestions.
I just tried lpa – it produces a decent alignment (nearly identical to the other things I tried that worked ok: default cost function with giant move/ ginormous move, nudging + those things)
I included a picture of this alignment. I have put the crosshairs where I see the main issue to be, that curved line looks like it should fit a nearby anatom
by
hdempseyjones
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AFNI Message Board
Hi Peter,
Thanks for getting back, here are some images (sorry I can never get the image upload in afni to work properly)
This is the problematic participant, P07_LV
With giant move - big fail
With ginormous move - better but still bad
Thanks for the link, that's where I got the idea for the nudge and 3dAllineate from - which works well for the problematic P07_LV (note
by
hdempseyjones
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AFNI Message Board
Hi there,
I have been trying to do an alignment with the following details:
- Anatomical to epi
- Partial coverage (I have a small epi slab centred over left SI)
- 7T data
I have two subjects, and things worked differently for the two. Only method 2 produced something that was not way, way off for sub2 where sub1 was generally ok with most methods (aside from method 3 & 5)
I h
by
hdempseyjones
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AFNI Message Board
Thank you Rick - normal processing seems to work fine, the wrapped bit of brain just disappears in the alignment step as we are aligning our epi to our anatomical
by
hdempseyjones
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AFNI Message Board
Sorry, here is link to the image, I cant get the embed to work
by
hdempseyjones
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AFNI Message Board
Hi there,
I have some nifti files that have the back of the brain cut off and wrapping around to the front of the image. It gets worse over runs, as it looks like the head moves back in the frame more over time.
I have the suspicion that this is caused by the FOV for the scanner not being positioned correctly - and then motion of the head backwards over runs making that worse. But I tho
by
hdempseyjones
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AFNI Message Board
Hi there,
Sorry if this is a very silly question but I am new to fMRI and just wanted to clarify something about event vs. blocked designs:
Some literature suggests that for a fMRI design we are planning, we should rapidly switch between our two stimulation types (vibratory stimuli of different frequencies, 3Hz for one condition, 30Hz for another).
Question 1.
If we present stimulation
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hdempseyjones
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AFNI Message Board
Thank you for the poster and info ptaylor, I will have a look into the correlational methods you suggested (and make sure to visually investigate my registration :) )
by
hdempseyjones
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AFNI Message Board
Hi Daniel,
Thank you for dealing with all of my questions across streams :)
Just wanted to confirm I have understood what you are saying in your reply:
For real data, to probe volreg success, enorm and similar values (like FD) are ok to use (in conjunction with visualisation) - ??
However, when using affine methods, such as when doing alignment with 3dAllineate, using these enorm/ FD
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hdempseyjones
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AFNI Message Board
Hi Daniel,
Thanks for your response. Sounds like issue with alignment using lpc+ZZ is related to partial coverage, as you say, so will leave it and use lpc, which worked ok.
---
Back to volreg for a second, when I use MIN_OUTLIER volreg, there is quite a lot of motion left *only* in my first run (all others are much improved, see image 1 below).
Image 1 – enorm for original data (blac
by
hdempseyjones
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AFNI Message Board
Hi there,
I have been wondering about how to compare different volreg methods to see which produces the best alignment. I have been looking in the GUI between and within blocks/ overlaying them etc. But I wanted a more quantifiable method
I was wondering if this approach, related to running volreg twice and comparing enorms makes sense??
This is what I did
1. Run my volreg1 using chosen
by
hdempseyjones
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AFNI Message Board
As a possibly related update - when I try and do volume registration with 3dAllineate using lpa+ZZ I get good registration but really weird clipping of the brain where, as I move to more sagittal slices, the front of the brain completely disappears (looks like a big black shape is moving from forward to back over the brain until you can't see it anymore).
So, alignment and volreg have i
by
hdempseyjones
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AFNI Message Board
Hi Daniel,
Thanks for your reply.
I think I will also leave the autoweight option alone: I don't have a specific autoweight setting in mind I wanted to use, I was investigating whether it could improve alignment (in light of the warning aea threw up).
Basically, I think my epi-anatomical alignment is ok (I am unsure if it is close enough as I am new to fMRI), but would love any
by
hdempseyjones
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AFNI Message Board
Hi Daniel,
Thanks for getting back to me
Looks like I will ignore the -obliquity -autoweight and -cmass options, as it is likely they are already being accounted for in my script.
I can see where deobliquing is taking place, and where cmass+a is being used in the output script, but no mention of -autoweight at all.
Question: Does this mean it is not being used, but is not needed?
by
hdempseyjones
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AFNI Message Board
Hi there,
I am using align_api_anat.py under afni_proc.py for some alignment of epi (partial coverage) to an anatomical
I am getting some warnings with my first pass (code below), and just wanted to make sure I am doing the right things.
The first warnings are about obliquity.
I get obliquity warnings about my epi (around 36 degrees from plumb) during most parts of the processing (3dT
by
hdempseyjones
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AFNI Message Board
Hi there,
I am using afni_proc.py for some pre-processing. I added -AddEdge as an option as part of my align_epi_anat block.
This has successfully generated a folder of edge images, but when it has run and I cd into the AddEdge folder, when I try to run @AddEdge -auto it throws up a bunch of different overlaid images one after the other, all disappearing quickly, leaving only my original an
by
hdempseyjones
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AFNI Message Board