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Dear AFNI users-
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Sincerely,
AFNI HQ
History of AFNI updates
We will try the "randomize" function but if I was to use the approach with 3dMVM -resid:
This gives me a _resid output file with 1800 values per voxel (we have 1800 subjects).
1) Should I loop through this sub-brik with 3dFWHMx, where the loop index is used to give 3dFWHMx one sub-brick at a time or can I just give it the full 4D-volume?
2) Should I use any of these option?
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Robin
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AFNI Message Board
Just want to thank you all for your very helpful input!
So very appreciated!
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Robin
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AFNI Message Board
Hi!
If I would have normal fMRI-data and run a factorial 3dMVM analysis I know the steps to get "valid" cluster-corrections using the errts-files to in 3dFWHMx -ACF to generate the acf-paramters followed by simulations in 3dClustSim where you have to pick a "maximum" a per-voxel threshold of 0.002 to be able to claim that the results are false-pos corrected according to AF
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Robin
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AFNI Message Board
I got a reply from the author of the longitudinal pipeline!
Hi Robin,
the long-processed images are all in the same space as the base image. This is -kind of- in the middle between your two time points (e.g. if the head is tilted left in TP1 and right in TP2 it will be upright) .
So if you want to use that mask in your fMRI analysis you need to register the fMRI with images from the base
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Robin
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AFNI Message Board
Hi!
QuoteJust as a nomenclature point, the "T1" in the SUMA/ directory is the one with "SurfVol" in the name, yes? We usually refer to that as the "SurfVol dataset" (for guessable etymology)
Not really, but they are basically the same. In the generated SUMA-dir we have:
ls ~/FREE_SURF/sub109/TP1/SUMA/
etc...
sub109_SurfVol.nii
T1.nii.gz
etc...
But they give
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Robin
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AFNI Message Board
Thanks Paul! Such good info!!
Your questions:
Quotept
To be clear, is "@Make_Special_FS" actually "@SUMA_Make_Spec_FS"? I am also confused by what "your" T1 is here.
Yes, I should have corrected that, it is @SUMA_Make_spec_FS.
The two T1-images I am referring to is
T1: our original T1-weighted MRI scan, I'll call it T1-orig from now on.
The other T1 is
by
Robin
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AFNI Message Board
Hi! This is regarding FreeSurfer + @SSwarper:
We have been pulling our hair out over wierd stuff happening. Following the guide, we simply run recon-all -all where we input our orig T1:
T1=/path/T1.nii
This generates the /path/freesurfer/subX dir where we run @Make_Special_FS command which generates the dir
/path/freesurfer/subX/SUMA where we find all masks/ROIs. Also, we find a T1.nii.gz i
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Robin
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AFNI Message Board
Hi Paul, thanks! Please see my latest post under Bob's reply! Would be very interesting to see your thoughts (on another issue - that we can totally move to a new thread!)
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Robin
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AFNI Message Board
Thanks Bob!
I am (g)root on the server and I think I used sudo killall afni.
The GroupIncorr issue:
I am sorry, this might have been incompetence... I just used one subject to create the GroupIncorr.niml/data files. Could that have been an issue? Bad data? We ran it now using 3 subjects and it work! Sorry!
The Instacorr Issue:
Yes! It was probably was the scaling! Is this a problem? Ru
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Robin
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AFNI Message Board
Thanks Paul!
This got a bit messy and turned into two questions:
1) InstaCorr:
It works. The problem was something else, which is strange. When setting up Instacorr, and mask is checked an automask = on, it turns out it makes an inverted mask! I get voxels/correlations if I place the marker outside the brain. If I turn off auto-mask, then I get values in the brain (and they make sense, e.g
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Robin
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AFNI Message Board
Thanks!
Will that kill any processing done by other users on the server? E.g. afni_proc?
Also, when you say that perhaps another instance is running, could that be by another user logged into the same machine?
Afni is installed for all users under /usr/local/abin.
Thanks for prompt replies!
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Robin
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AFNI Message Board
Hi!
I have used InstaCorr and 3dGroupIncorr before and it has worked great. I now experience some similar problems between the two functions and suspect something is wrong. Or, I just forgot how to use it.
lsb_a -release
Distributor ID: Ubuntu
Description: Ubuntu 18.04.2 LTS
Release: 18.04
Codename: bionic
afni -version
Precompiled binary linux_openmp_64: May 29 2021 (Version AFNI_
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Robin
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AFNI Message Board
Hi!
We do use the @SSwarper function in our normal fMRI pipeline (yes, it is amazing!). But this is for another project where I just want skull-stripped brains in native space (no non-linear warping) since we want to use them for classification in a 3D CNN. If we use non-linear warping we will potentially lose the differencies between the patient group and HC that we are investigating. This is w
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Robin
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AFNI Message Board
Hi!
I am running skullstripping on a large (>2000) T1w images from different sites and hence different image parameters. I started using the FSL bet function since we plan on using the FSL VMB function package later on and I found that for some datasets there is always a quite large chunk of tissue left form the area that is between the brain and spinal cord (left of the CSF that is left of
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Robin
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AFNI Message Board
Thanks! That gave similar results. But I had to use the -cm option in the @AlignCenters functions, otherwise the brain stays where it was in space (e.g. low in y-dim). Perhaps due to the native images having its center at the matrix center? Anyways, this worked:
for i in * ; do
@Align_Centers -cm -base $template -dset $i -prefix ../$out_dir/temp_$i
3dresample -master $template -inset .
by
Robin
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AFNI Message Board
Thank you!
But then it sounds like my approach is correct.
I wanted my varying native resolution data to all have the same resolution (192,224,192) and that the brains are placed at the center of the volumes so that they all somewhat overlap.
But a simple 3dresample command gives me the correct grid but the brains are not moved to the center (of course)
And a simple 3dresampel comman
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Robin
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AFNI Message Board
Doesn't that only move the center of the image (e.g. move the center from center of mass to center of the volume) but not moving the data itself?
Doing a simple 3dresample command is problematic since that can cut of parts of the brain. What seems to work is this:
for i in * ; do 3dAllineate -cmass -warp shift_only -base ../new_template.nii.gz -source $i -prefix rs_$i ; done
The -war
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Robin
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AFNI Message Board
Hi!
I have a large set of T1-scans from different sites which I have skull-stripped GM-extracted (i.e. I have a set of GM-maps) that are all in native space, no warping has been preformed. That means that some of the brains are pretty far of the matrix-space center.
I am going to run augmentations on these so it is important that they somewhat overlap in space and since I will run rotationa
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Robin
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AFNI Message Board
Hi Paul, chiming in here (Irene and I are form the same lab and we are using the script we ended up with after my last thread). If I remember correctly we talked about how to handle obliquity. I used one of your options from here, i.e. purging the obliquity information.
Firstly I attach a print of the tempalte with test_copy.nii as the overlay generated by:
3dcopy ${T1_data} test_copy.nii
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Robin
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AFNI Message Board
Hi Rick! Ah that's good =).
1) I think it's the align part since it says "+ * Enter alignment setup routine" a few rows over the errors. It seems like the automatic review part (reading the cost file) fails since it prints the same cost for boths flips which I guess are the default or starting costs of 1000. I'll email you the full output but it should also be in the o
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Robin
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AFNI Message Board
Sorry for a rude bump of my own post here but there were a few things that were not cleared out:
1) The errors in the output related to the check-flip option:
++ Writing -allcostX1D results to '__tt_lr_flipcosts.1D'
+ - histogram: source clip 288.416 .. 1065.28; base clip 196.319 .. 848.294
+ - versus source range 1.69773e-05 .. 1148.31; base range 0 .. 934.575
+ 53147 tot
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Robin
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AFNI Message Board
Wow, what en helpful answer. Assuming the follower T1 looks good after I implemented -deoblique_refitly as an SSWarper option this really helped me understand what deoblique means as well.
Big thanks!
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Robin
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AFNI Message Board
Good that the information was relevant =).
While I'm waiting to hear from the potential flip-cost-file-read error and for someone else to answer the other 2-3 questions I looked at the output of the follower dataset. I followed the example and the relevant code bits are here:
#Original NIFTI
T1_data=$datapath/T1.nii
#SSWarperCommand
@SSwarper -input $T1_data -base /usr/local/abin
by
Robin
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AFNI Message Board
(QuickFix for that issue, since my collegue actually runs this from two servers with the same target directory. Just create and cd into the output dir of @SSwarper)
startdir=$(pwd)
datapath=/home/robka/full_task_preproc/data/C_sub${sub}_EB
T1_data=$datapath/T1.nii
mkdir pre_warp_$sub_id
cd pre_warp_$sub_id
@SSwarper -input $T1_data -base /usr/local/abin/MNI152_2009_template_SSW.nii.gz -
by
Robin
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AFNI Message Board
Thanks!
That's all I wanted to hear :). We have tried to dabble with ETAC but found it still to be very conservative. But that was in the early days, perhaps time to give it a new go! =)
Something I noticed as a bonus:
Not sure this was from @SSwarper of afniproc since my script is running them in sequence but one of those processes created temp-files in the directory where I run m
by
Robin
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AFNI Message Board
Great, thanks!
I looked and the unflipped was indeed better. But would be really nice if you could check if there is a bug or implementation fault from my side!
I also noticed that in the suggested proc blurring was used with a 4 mm setting. We kind of have a debate here regarding blurring/smoothing.
In a sense the data is already blurred biologically, MR scanning and then normalization.
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Robin
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AFNI Message Board
Hi AFNI experts,
Due to my previous questions regarding bugs in the update we realized we had not followed the development of new recommendations for a typical task pre-proc pipeline. Rick kindly refereed me to:
afni_proc.py -show_example 'example 6b'
And I also read the SSwarper documentation. All the changes make sense to me but it leaves me with a couple of questions.
Just a
by
Robin
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AFNI Message Board
Awesome! Thanks!
You guys were, as always, super helpful and quick!
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Robin
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AFNI Message Board
Thanks Rick! You beat me to it. Found that the script used the MNIavg template.
We usually use the MNI152_2009_template.nii.gz as the basis. But this new approch looks interesting. I guess we should implement that. Thanks!
by
Robin
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AFNI Message Board
I looked into the T1-image quality thing too.
I personally think (look at cerebellum) that the T1_al_junk (left) looks better than the anat_final.test image (right). I want to remember those warped T1s (anat_final and anat_final_w_skull) looking more clear. We do use -volreg_align_e2a \.
Doesn't it look kind of low-res? Input T1 is > 1mm reslution isotropic and and anat_final.test i
by
Robin
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AFNI Message Board