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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:
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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
Page 2 of 4
Pages: 1234
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thank you that works fine!
final question, supposed that I modified in a second step the origin of dset_anat_deob to fit the template
3dCM -set 0 0 0 dset_anat_deob
and measure the transfo as Anat_rs_tshift_deob_RECEN.1D
to realign dset_bold_deob I do:
@Align_Centers -overwrite -base dset_anat_deob -dset dset_bold_deob -prefix BOLD_rs_tshift_deob_RECEN.nii.gz -shift_xform_inv Anat
by
Doughboys
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AFNI Message Board
Sure the command
afni_proc.py -subj_id Oliver2019_02_02 -script \
proc.Oliver2019_02_02
-scr_overwrite -out_dir \
/Oliver2019_02_02.results \
-bloc
by
Doughboys
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AFNI Message Board
my previous misunderstanding makes sense now!
Is my correction with "3dWarp -oblique_parent" ok?
or is it a problem to blur a little bit the functional before passing it into afni_proc.py?
Do I have another solution? Can I concatenate the difference of obliquity directly with the WARP or AFF included in afni_proc.py to not accumulate multiple transformations?
or should I not do &qu
by
Doughboys
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AFNI Message Board
I got it!
So for future users,
just do:
3dWarp -overwrite -gridset dset_bold_deob -oblique_parent anat -prefix dset_bold_deob dset_bold_deob
before
3drefit -overwrite -deoblique dset_func_deob
anat being dset_anat_deob before deboblique
Cheers,
Clem
by
Doughboys
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AFNI Message Board
Hello Paul,
I have done A) already, using Daniel's previous advice but sadly the results were incoherent with what I obtained using a classical atlas-based quantification.
The B) seems logical to me, and I will try it.
However, I have to say that I don't get how inverting the AFF and combining it with the original AFF will exclusively remove the rotations?
Otherwise, that s
by
Doughboys
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AFNI Message Board
Hello AFNI team,
When removing obliquity from my original images (just converted DICOM to Nifti) using the command:
3drefit -overwrite -deoblique dset_anat_deob
for anatomical images (deobliquing the anatomical images before @animal_warper was advised in a previous post)
and
3drefit -overwrite -deoblique dset_func_deob
for functional images
Originally (before deoblique) dse
by
Doughboys
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AFNI Message Board
Hello,
It seems that the only way to deactivate the EPI skullstrip in afni_proc.py is to put both align_epi_strip_method None and -epi_strip None.
If I am right, this is a little bit confusing (it took me a while to understand what was going on)
Clem
by
Doughboys
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AFNI Message Board
For info:
I tested both methods without changing any parameters.
The result seems good and no significant variations were found between the two methods.
Thank you!
Clément
by
Doughboys
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AFNI Message Board
Hello Daniel,
No, it doesn't create any problem (so far)
I was just wondering what parameters did you put in your example in order to avoid to re-invent the wheel especially since I am really not sure what they do exactly and what will be the impact of changing them.
Any proposition to try at first for
-resample
-maxthick
and
-depthsearch
I will definitely try @measure_erosion_t
by
Doughboys
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AFNI Message Board
Hello AFNI team,
Is it necessary to change default parameters in @measure_bb_thick in macaques as in :
I am thinking of:
-resample
-maxthick
and
-depthsearch
The program is particularly long in my case
I am using masks of 0.5mm isotropic
Thank you all!
Clément
by
Doughboys
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AFNI Message Board
Hello Gang,
Sorry to come back AGAIN with a new question.
When thinking about it (it happens sometimes =)) I realize that maybe I should add a session effect to my model.
Since all the animals were scanned on the same day it may affect the result.
However, the session is strongly linked to "age" and I don't want to annihilate my findings by adding "session".
What ar
by
Doughboys
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AFNI Message Board
I will try that, it makes sense to me!
Thank you Daniel!
by
Doughboys
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AFNI Message Board
I confirm that pre-aligning the images and using "-align_centers_meth OFF" fixed the problem.
I have the filling that an extra shift is added when passing the image into 3dAllineate.
maybe an error in cat_matvec?
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I plan to measure the Jacobian with 3dNwarpFuncs (from individual space to template).
I am confused about the correct WARP for this analysis in order the measure the deformations to the template.
can you confirm that the correct WARP to use is?
_shft_WARP.nii.gz
thank you
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I am having a few problems aligning macaques anatomical T1 to the template (3 out of 90 success, not bad!)
to resume:
- something not normal with aff_move_opt. It seems that you can only use one option and not combine multiple ones.
- _shft.nii.gz (not sure actually what is the command is producing this image) = far from the BASE. The orientation of the brain in T1 is not
by
Doughboys
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AFNI Message Board
Ok no problem, I see that the discussion is expending a little too much =)
by
Doughboys
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AFNI Message Board
For the Jacobean, you certainly *don't* want the global translation and rotation included (those are the rigid body parts of the transform).
Sure this is what I thought, but I was confused when you said: If in subject space... no issues.
do you want the global shear and scaling from the affine, as well as the local displacements from the WARP, or just local displacements themselves?
by
Doughboys
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AFNI Message Board
Update,
I actually still have the problem (a few co-registration misalignments) of macaques anatomical T1 to the template (out of 90 success, not bad!)
to resume:
- something not normal with aff_move_opt. It seems that you can only use one option and not combine multiple ones.
- _shft.nii.gz = far from the BASE. The orientation (mostly in SI axis in my case) is not correct (not sure actual
by
Doughboys
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AFNI Message Board
Hello,
So, I actually find that the mistake was coming on my side (my study template was not centred on 0).
Animal_warper seems to have worked without problems on 90 macaques images... I still need to validate that precisely =)
Note that, I previously skullstrip and centred on 0 my original anatomical images before passing them into animal_warper
Just to clarify my previous question,
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I would like to use a WARP in tlrc_NL_warped_dsets the has been created using 3dNwarpCat.
This WARP originated from multiple .1D and WARP files and works perfectly when used with 3dNwarpApply.
The problem is that if I only input 1 WARP (and the anat file) in volreg_tlrc_warp, it doesn't work because volreg_tlrc_warp needs 3 files.
Can I add a .1D file with just 0?
by
Doughboys
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AFNI Message Board
thanks, Paul!
I was using the shft_WARP provided by animal_warper, so I should use _shft_base2osh_WARP (this is the only WARP in the indiv space) instead in 3dNwarpFuncs? and then send the Jacobian in the template space?
I am trying to identify more precisely what is wrong with @animal_warper, I will give updates if I managed to find it, do you have any suggestions?
I just find somethin
by
Doughboys
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AFNI Message Board
Hello,
I am also facing the same problem
I will try your fix tomorrow, thank you
As far as I remember this recent modification was made to automatically recenter the anatomical image to the template
Something might be wrong with it.
Also, I was wondering if the scaling or shearing performed in align_epi_anat.py would modify any volume quantification performed when using VBM with on the ext
by
Doughboys
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AFNI Message Board
Hello AFNI team,
It seems that the option -qw_opts in @animal_warper doesn't work.
I systematically got:
** unknown option -qw_opts
when trying to use it.
I am working on 'Version AFNI_21.2.03 'Nerva''
Clément
by
Doughboys
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AFNI Message Board
Hello Pawel,
exactly
3dSkullStrip, -skullstrip_opts -monkey and cost lpa+ZZ did the trick (I also used -resample off).
Happy to help you!
by
Doughboys
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AFNI Message Board
Yes, I think that this one has MION (I need to ask...)
However, my guess was good!
lpa+ZZ associated with the option -monkey did the trick for those who it didn't work previously!
by
Doughboys
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AFNI Message Board
Hello pt!
Thank you for your answer that will really help!
Here is an example of the kind of image that I am working with:
Indeed, I was already using -cost lpa+ZZ that is actually working fine on half of the images. lpc+zz and nmi doesn't work at all.
I am confident that changing the epi strip parameters might help!
I will let you know
Thank you for explaining align_epi_strip_
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I would like to "classically" co-registrate a BOLD image to a template using the movement parameters of the anatomical image, in a primate, with afni_proc.py.
for a typical command please see:
I would like to know if there is a way to modify the "3dSkullStrip or "3dAutomask" parameters in -epi_strip of afni_proc.py?
For example, if I would like
by
Doughboys
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AFNI Message Board
Hello,
Still stuck with that problem.
Any idea of what I could do to fix it?
Thanks!
by
Doughboys
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AFNI Message Board
Hello,
>Thank you, I was not sure about this. I replaced it but it did not change anything on the error message.
Thank you for your help!
Clément
by
Doughboys
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AFNI Message Board
Page 2 of 4
Pages: 1234