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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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Thanks, you are right on all accounts. The spatial transformation works but the tensors need to be reoriented as well. WIth ANTs one can use ReorientTensorImage but this needs the transform that was applied to the volume and it doesn't seem to work with afni's 1D transform files. Maybe, I should move this whole routine to ANTs and stop trying to make the afni transforms work in ANTs.
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ChrisKlink
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AFNI Message Board
Using nifti_tool to edit the header seems to solve the issue. I will now close this dialogue with myself on the message board and hope it will be useful for someone in the future
nifti_tool -mod_hdr -mod_field intent_code 1005 -infile IN.nii -prefix OUT.nii
by
ChrisKlink
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AFNI Message Board
When I compare headers, these are the differences:
Before 3dAllineate
name offset nvals values
------------------- ------ ----- ------
intent_code 68 1 1005
datatype 70 1 64
bitpix 72 1 64
after 3DAllineate
name offset nvals values
------------------- ------ ----- ------
by
ChrisKlink
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AFNI Message Board
Ok, the '3dAllineate not being capable to save' was my mistake. I can actually use 3dAllineate on the 5D tensor file but the output has a different datatype than the source (Float32 instead of Float64) and the result is now no longer seen as a tensor volume, but instead as scalar. Maybe this is where things go wrong?
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ChrisKlink
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AFNI Message Board
I feel like I'm missing something obvious, but here's my situation: I have warped the ONPRC18 dti template of the rhesus macaque to NMT using the RheMAP based transforms I previously calcuated with ANTs (antsApplyTransforms). Now I want to incorporate this in our 'single-subject pipeline' that uses @animal_warper to align NMT/CHAR/SARM to the individual so that I also get a co
by
ChrisKlink
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AFNI Message Board
I have had good results using @animal_warper with cost lpc on T2w scans of NHP with implants. No crazy hyperintensities though, but I suppose the masking approach might help you out there...
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ChrisKlink
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AFNI Message Board
I was wondering if there are any tricks for getting @animal_warper to work better with T2w images? I tried setting the cost to lpc+ZZ and that improved things but it's still not great. The white matter aligns reasonably well in some spots but the gray matter is pretty off (brain size overestimated). Maybe the scans I received to process are simply too bad for this to work, but I feel it has
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ChrisKlink
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AFNI Message Board
No leads? I haven't been able to find the cause myself either and although it is bugging me a bit, the fact that I somehow got it working lowered the urgency for me...
by
ChrisKlink
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AFNI Message Board
If I do a 3dAllineate on the volume before feeding it into @animal_warper, I still get the same error.
3dAllineate -source SingleSubject.nii.gz -base NMT_v2.0_sym.nii.gz -prefix SingleSubject_al.nii.gz -cmass -warp shift_rotate -overwrite -float -newgrid 0.5
The resulting file looks good and indeed pretty well aligned with the NMT. Within @animal_warper intermediate results, the pshft file
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ChrisKlink
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AFNI Message Board
Thanks Paul, I suspect it's not the realignment per se, but perhaps something else changes in this step to. If I remember correctly I first tried realigning in fsleyes and got the same error, while after realigning with things ran without hick-ups. It's probably something stupid, but it would be good to know what's happening. I'm prepping an info package for you with exact co
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ChrisKlink
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AFNI Message Board
I did a manual translate and rotate again to bring the single subject volume close NMT and now it seems to work (running the 3dQwarp step now and intermediates look good). Still a bit confused about what's happening, but at least we're getting there...
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ChrisKlink
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AFNI Message Board
Hi all,
I've been using @animal_warper with much success for a while now, but yesterday I encountered a weird error.
The first *ERROR* in the output reads:
** FATAL ERROR: 3dQwarp fails :: source has 0 nonzero voxels (<100)
I backtraced this and it seems that things go wrong at a an early 3dAllineate step for affine registration. The 'shft' and 'psift' volum
by
ChrisKlink
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AFNI Message Board