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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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Hi Rick,
Thanks for the info and quick reply. In reading further, it looks like OpenMP 4.0 and above will work for offloading to the GPU instead of CPU. I'm looking into implementing this on our HPC environment (RedHat) and further down the line a docker or singularity container. For the container route I was initially looking at CentOS since it aligns better to RHEL but I'm not
by
AjaySK
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AFNI Message Board
Hi Afni Experts,
I wanted to find out which version of OpenMP is used in the precompiled code (MacOSX and linux) and if it is possible to use openmp 4.5+ with AFNI built from source code? The reason I ask is that OpenMP 4.5+ supports use of GPUs for parallelization with minimal edits so I was curious to looking into this further.
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hi Bob,
I came across what fixed the issue. It looks like from my original post I was missing an -emask option that was in the code that actually crashed (I accidentally missed that option when typing my post), and once that was removed it ran fine. Since the images were close to begin with and the mask was tight, that may have made a difference in this boundary case.
Thanks again for
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AjaySK
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AFNI Message Board
Hi Rick,
Thanks for the feedback. It makes sense regarding no major differences between AMD vs Intel.
In terms of RAM my question it was not 4GB total per node but 4GB/physical core/node. Since a dual socket node with 52 cores (intel 6230R x2) that would be 208 GB ram which is doable if we need 4GB/core/node. If I go with AMD which is 128 cores (64 cores x2 cpus) this would be 512GB w
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AjaySK
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AFNI Message Board
Dear AFNI experts:
I am designing a new neuroimaging cluster and wanted to see if there is a recommended RAM to core recommendation for AFNI. Generally I have purchased systems with 4GB ram per core but the current core count on this new system is about 52-64 cores per node (hyper threading disabled) so I am wanted to get more feedback as that can be a pricy endeavor. Is there a recommende
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I wanted to follow up to see if there were any insights into the problem. Thanks for the help.
Best,
Ajay
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I am using 3dQwarp and for most subjects it runs fine but I had a handful that would fail. Below is the error I am seeing. My guess is that the start and stop cost are close enough for the patch that it triggers a fail but that is just my hypothesis. This error is on AFNI_21.1.20 and 20.0.18
3dQwarp -prefix ./anat.rw.qw.nii -workhard:0:1 \
-penfac 1 \
-maxlev 4 \
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AjaySK
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AFNI Message Board
Thanks for the info. I updated it and the new version (20.0.18) and it is now working.
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hello AFNI Experts,
I think I have come across a bug in auto_warp.py on the latest release related to the skip_affine flag. I ran the following:
auto_warp.py -base MNI.nii -input T1.nii -warp_dxyz 1 -skip_affine no
I received the following error:
else: endif not found.
ls: cannot access anat_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft.1D: No such file or directory
** ERROR: mri_matrix_evalrpn(&
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AjaySK
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AFNI Message Board
Hi Bob,
Thanks again for the suggestions. I agree it is great to incorporate but there are definitely several technical challenges such as dealing with differing distortions between modalities (i.e. diffusion vs fMRI vs structural) that will make it a bit more challenging , along with system requirements. Maybe limiting it to structural scans with little distortions such as T1/T2/proton den
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AjaySK
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AFNI Message Board
Hi Bob,
Thanks for the explanation on how the weighting etc works within the program. I was using my own weight to emphasize areas where alignment is most crucial when warping. When reading through the emask option and testing with the default .4 clip fraction from 3dAutomask I worried that one of the areas in the brainstem would be excluded that I am emphasizing, which is where my questio
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AjaySK
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AFNI Message Board
*Note*
This question has been split into a separate thread from where it was originally asked (which was here: ).
It is a separate question, so it should have its own thread. In the future, please address new questions with separate threads, for readability.
--pt
--------------------------------------------------------------------------------------------------
Hi AFNI Experts,
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I checked with AFNI version 18_2_13 (version without -lite flag) and it works fine, so it seems like with the new version (19.1.08) the minpatch willl not go to a lower resolution than what the iniwarp ended at, but still outputs a warp file. Hope this helps in the troubleshooting.
Best,
Ajay
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I'm using AFNI's latest linux_openmp64 binary (19.1.08 'Caligula'). I ran a warp field at minpatch 11 and later used that warp field as an iniwarp parameter in 3dQwarp (via auto_warp.py by specifying options). My commands are registered and the output notes reflect all parameters were passed without issue.
3dQwarp -prefix anat.rw.qw ./anat.rw.qw.nii -
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AjaySK
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AFNI Message Board
Hi Daniel,
Thanks for the suggestion!
a) It seems that when there is only rotation the upper and lower triangle (3x3 matrix) are symmetric aside from the sign flip.
1dApar2mat 0 0 0 -0.081944 -0.103117 -0.169312 1.000000 1 1.000 0 0 0
# mat44 1dApar2mat 0 0 0 -0.081944 -0.103117 -0.169312 1.000000 1 1.000 0 0 0 :
0.999995 -0.001425 0.002955 0.000000
0.001430
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AjaySK
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AFNI Message Board
Hi Daniel,
I have a follow up question of how the affine matrix is organized based on the documentation below:
----------------------------------------------
DEFINITION OF AFFINE TRANSFORMATION PARAMETERS
----------------------------------------------
The 3x3 spatial transformation matrix is calculated as ,
where is the shear matrix,
is the scaling matrix, and
is the
by
AjaySK
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AFNI Message Board
Hi Peter,
I also tried using 3dNwarpCat to combine the transforms and warp and had the same issue. Do 3dNwarpCat and 3dNwarpCalc function differently? I
Best,
Ajay
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I had a subject that I ran auto_warp.py once and the outputs had some line/vein artifacts. I took that output and ran auto_warp.py once more and the results came out great. When I concatenated the second set of transforms to apply to the original output of the first auto_warp.py things looked great. (3dNwarpApply -nwarp 'anat.rw.qw_WARP.nii anat.aff.Xat.1D'
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AjaySK
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AFNI Message Board
Thanks for the suggestion Daniel I will try it out.
I had one general question regarding some of the outputs with 1Dmatrix_save and -1Dparam_save.
Specifically when looking at the rotation matrix (param 4-6) from 1Dmatrix_save and the x,y,z rotational components in 1Dparam_save I could not get them to match exactly. When I converted the param rotational components from degrees to radian
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AjaySK
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AFNI Message Board
Hi AFNI experts,
I am running into an issue for applying some transforms. I have a T1 brain which I have rigidly aligned to my EPI scan (tx_1.1D) with the cmass flag in 3dAllineate. I have that same T1 brain also rigidly aligned to the MNI template for AC-PC alignment (tx_2.1D) using -cmass. I use cat_matvec to combine the transforms as follows:
cat_matvec tx_1.1D -I > tx_1_inv.1D
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AjaySK
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AFNI Message Board
Hi AFNI Experts,
I just wanted to follow up to see if there were any issues using vecwarp with ASL orientation and the 3dAllineate matrix alignment (RAI dicoms orientation) directly to MNI space to correct bvecs for the rotation or if I have to account the initial ASL orientation of the dataset somehow prior to vecwarp.
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hi AFNI experts,
I had a question regarding vector orientation information when applying MNI transforms to DTI data . I have a file that is eddy current corrected and its corresponding bval/bvec corrected files in subject space. I have a T2 image that was then aligned with the DTI data. The original brain (not B0 aligned) is also rigidly aligned to the MNI template and then ran auto_warp
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AjaySK
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AFNI Message Board
Hi Bob,
Thanks for the followup and other options. I saw this after I sent my message on 3dAllineate. I'll try it out!
Best,
Ajay
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AjaySK
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AFNI Message Board
Hi Bob,
When using B0ref.nii as the base and B0vols.nii[0] as the source (all same resolution), I assumed that this would potentially mitigate any underlying issues of the 3dAllineate -nwarp bilinear warp field being created from different resolution datasets being off.
Interestingly, when I used 3dNwarpApply on the resulting warp field the image looked correct except that it was shifted i
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AjaySK
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AFNI Message Board
Hi Bob,
I was planning on using this same step with my resting state analysis to better account for geometric distortions on this dataset that does not have a field map to my mean EPI image. Since the bilinear option seems quicker than 3dQwarp for this step i figure I can test on the DTI since the distortion on this subject is slightly worse than the resting state scan but definitely would
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AjaySK
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AFNI Message Board
Hi Bob,
Thanks for the help. I sent you a PM with the link to dropbox.
Best,
Ajay
by
AjaySK
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AFNI Message Board
Hi Bob,
I was looking at bilinear for eddy current correction to test against affine to see if it was much better or not. I ran into a strange problem. I ran the following:
ind=0
while [ $ind -le 60 ]
do
3dAllineate -base B0ref_resamp.nii.gz -source dwi.nii[$ind] -master BASE -prefix eddy_${ind}.nii -1Dmatrix_save dwi_${ind}.aff12.1D -1Dparam_save dwi_${ind}.param.1D -nwarp_save warp
by
AjaySK
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AFNI Message Board
Hi Afni Experts,
I wanted to follow up with my original email below to see if anyone had any thoughts/guidance.
Thanks,
Ajay
I am interested in combining subject level corrections using quadratic corrections (3dAllineate -nwarp option with bilinear) with my warps to MNI which are derived from auto_warp.py. In this case, instead of having just the 3dAllineate affine .aff12.1D fil
by
AjaySK
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AFNI Message Board
Hi Afni Experts,
I am interested in combining subject level corrections using quadratic corrections (3dAllineate -nwarp option with bilinear) with my warps to MNI which are derived from auto_warp.py. In this case, instead of having just the 3dAllineate affine .aff12.1D file, I will have a parameter file instead.
1) If I wanted to combine 3dAllineate parameter file with my 3dQwarp warp f
by
AjaySK
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AFNI Message Board
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Pages: 12345