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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
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Thank you for your answer.
For the local deformations, which warp should be used to get the correct values if a brain is warped to a brain atlas? forward or inverse?
I am using 3dNwarpFuns -bulk and would like to see which parts of the brain are smaller/larger compared to this atlas.
Atlas is the -master dataset.
by
mabbasi6
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AFNI Message Board
Hi,
Thank you for your response.
So, when I calculate the Jacobian of the warp, I have two options: Using the forward warp or inverse warp.
Imagine I am registering a subject brain to Allen Brain Atlas and I would like to see which parts of the brain are shrunk or enlarged compared to this atlas which is the master dataset as well.
I calculate the Jacobian with the 3dNwarpFuncs function a
by
mabbasi6
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AFNI Message Board
Hi all,
I have a question that is not specifically related to AFNI but has been confusing me recently.
Consider warping brain A to a brain atlas, and wanting to see the brain volume differences of brain A compared to this atlas. Does Jacobian of this warp show it or should I compute it for the inverse warp?
by
mabbasi6
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AFNI Message Board
Hi,
I have two groups of brains registered to an atlas and calculated the Jacobian for the transformations. I'd like to measure the effect size (Cohen's d in this case) for the Jacobians. How could I do that in AFNI?
Momo
by
mabbasi6
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AFNI Message Board
Hi,
Thank you for making the Allen mouse template available.
I have been warping some of my mice brain images to the CCF3, and the warp is working great (using either auto_warp or @animal_warper). However, the Allen template and the annotation have been taken to the Talairach space. Is there a way to take it out of talairach (to orig space)?
I have tried this function:
3drefit -view
to c
by
mabbasi6
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AFNI Message Board
Hi,
Thank you for your response!
I ran the command you suggested and the output was:
1.12356 0.00500563 0.0739877 6.93706 0.035566 1.07698 -0.170503 12.3146 -0.0403194 0.129099 1.12266 -6.46164
I have also been trying to warp step by step by aligning the center of my image (orig space) to the desired template (which is Allen CCF3 in tl
by
mabbasi6
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AFNI Message Board
I suspect that the fact that my input and base are in different spaces might have caused this (input in talairach and base in orig space).
Would you please let me know how this issue can be addressed?
Momo
by
mabbasi6
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AFNI Message Board
Dear Paul,
Thank you for your response.
I am using the 20.1.11 version, and I tried the same code you provided with 3dNwarpApply function. However, this function does not take .1D files as input and the error I receive is that the "process was killed". Instead, I tried running 3dAllineate and 3dNwarpApply separately, with .1D files as the input for 3dAllineate and the _WARP.nii.gz f
by
mabbasi6
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AFNI Message Board
Hi,
I have been using the @animal_warper function to align a mouse brain template to my mouse brain images and it has been working very well. The problem is that applying the same linear and non-linear warps derived by this function (by using -ok_to_exist) to the annotations (or even the same) image does not take me to the same final result as the function itself. Would you please let me know
by
mabbasi6
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AFNI Message Board
Hi,
I have been trying to register some mouse brain images to the Allen Mouse Brain Common Coordinate Framework v3 brain template.
I started by converting the NRRD format to NII using the 3dSlicer software.
After that, I downsampled the Allen CCF to 75 micrometers to match our data using the 3dresample function.
Then, I tried aligning the centers of the images but the @Align_Centers functio
by
mabbasi6
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AFNI Message Board