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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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Pages: 1234
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Sure,
for example, I have a human PET image, with its associated SNR and resolution.
I have a PET image in mice but with a lower SNR and higher resolution.
I would like to add "noise" to the human image in order to fit the mouse SNR and maybe signal distribution.
I hope that this is clearer
by
Doughboys
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AFNI Message Board
Dear AFNI team,
I am looking to downscale an image (PET, BOLD) to a lower resolution in order to match images with a lower resolution and SNR.
I am using images from different species, scanned with different machines, with very different SNRs.
Can you think of a meaningful way of downscaling a high resolution/SNR image to match an image at a lower resolution and SNR that would make them m
by
Doughboys
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AFNI Message Board
I think you are right,
the info I was getting on which hemisphere is which was not clear.
I will test a dataset with noticeable differences LR to check and resolve that issue.
Thank you again and sorry for the confusion =)
by
Doughboys
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AFNI Message Board
To complete these:
I have 3 datasets where the original orientation was RAI for 2 species (pigs and dogs) and LPI in another one (mouse lemurs)
The correct correction (except for LR since I don't know) was:
3dresample -orient RAI -input DSET_01 -prefix DSET_02
3drefit -orient LSP DSET_03
and 2 species (mice, rats) where the original orientation was LPI.
The correct correction (ex
by
Doughboys
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AFNI Message Board
Also,
to start answering question 3 (I may have understood a bit or maybe not )
The idea with the ptaylor strategy is that whatever is the original orientation specified by the scanner (or the header)
if the animal was in sphinx position and if you reorient the dataset in RAI with
# reset the orientation to something simple
3dresample -orient RAI -input DSET_01 -prefix DSET_02
the sec
by
Doughboys
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AFNI Message Board
Thank you both for your responses,
I think the reason why I could not understand the purpose of:
# reset the orientation to something simple
3dresample -orient RAI -input DSET_01 -prefix DSET_02
is because we may not use the same method to redefine the correct orientation.
What I am doing, is that I identify the brain orientation of y=1 and z=1.
For example in my case:
y=1 correspond t
by
Doughboys
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AFNI Message Board
Thank you for your answer pt,
That clarifys the process,
However, I am still not sure which one is the true right and left. Also, link to my first inquiry, I still struggle to understand why 3dresemple change the outcome of this.
Thanks again.
by
Doughboys
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AFNI Message Board
Hello Paul,
yes, this is exactly what I am trying to do (the "center of mass" part was also part of my process ).
I am working here with PET FDG dataset on rats, that I believe are in sphinx position (that would make a lot of sense).
However, I am not sure I understand the purpose of the command
3dresample -orient RAI -input DSET_01 -prefix DSET_02
When I apply it (as ad
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I have a simple (but crucial) question concerning 3drefit,
I received a dataset with incorrect header information (in particular L and R are FOR SURE reversed but not only).
Using 3dinfo the original orientation was LPI,
Using the command
3drefit -orient LSP -deoblique
I have now an image in the correct orientation for SI and PA, however, I still don't kno
by
Doughboys
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AFNI Message Board
Hello AFNI team (probably Gang ),
If you are performing a t-test (3dttest++ for example) between two groups of old and young age.
Would you add age as a covariate?
I would bet not since age is not independent of the 2 variables tested right?
I just wanted to be sure,
Thank you
Clément
by
Doughboys
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AFNI Message Board
thanks for your answer,
I used the atlas mask for 3dCM which actually did not give me a big difference when used on the template.
Clément
by
Doughboys
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AFNI Message Board
Hello AFNI team,
I would like to create a left and right hemisphere atlas and add 1000 to the Right hemisphere.
atlas_L.nii.gz is the left hemisphere image.
atlas.nii.gz the entire atlas.
I first tried:
3dcalc -a atlas_L.nii.gz -b atlas.nii.gz -expr "(b-a)+(step(b-a)*1000)" -prefix atlas_R.nii.gz
and it didn't give me any logical result when:
3dcalc -a atlas
by
Doughboys
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AFNI Message Board
The solution came to me last night, AFNI has somehow haunted me
I simply used 3dZeropad to remove the directions (A,P, I, L...) that were in excess.
In the end, I have got a smaller image centered in the brain.
Just to confirm, except for the fact that I have changed the image size does that make sense?
Thanks
by
Doughboys
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AFNI Message Board
Hello Afni team,
I would like to modify an atlas that was not centered on its center of mass.
using the following command line 0 is now the center of the atlas.
3dCM -set 0 0 0 img_master
However, how can center the atlas in the center of the image (the center of mass in the center of the FOV)
thank you very much
Clément
by
Doughboys
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AFNI Message Board
sorry to come back on my previous question,
thank you again for your time!
Clément
by
Doughboys
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AFNI Message Board
thank you, Daniel!
SurfaceMetrics and SurfMeasures did really work well!
What would be the unit of the result then?
For this question:
"If it is possible to do it with my WARP files, what would be the correct command line?"
I was wondering if there is a way to apply a classical afni "WARP" to a surface file like a .gii?
Finally,
sadly I am not sure that I un
by
Doughboys
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AFNI Message Board
Thank you, Daniel!
I now understand better SUMA!
However, if I am not mistaken, 3dVol2Surf allows converting a volume in surface, if in the same space right?
My problem is that my atlases are in the subject space (to measure the surface of each individual).
Is there a way to apply the WARP (template to the subject) that I generated for each subject to the Charm surface atlas?
From wh
by
Doughboys
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AFNI Message Board
hello AFNI team,
I would like to perform surfaces measures on an atlas co-registrated into the individual space (not the template space).
Basically, I would like to have a value for each region of the atlas representing a surface index. Is it something that is possible in AFNI?
I guess I have to go through SUMA? however, I am not very comfortable if that (yet!)
Any advice? tutorial online? o
by
Doughboys
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AFNI Message Board
Hello Gang,
Thank you
Subj age Sexe InputFile
Oliver 40.0 M Oliver2019_06_01/dir_D99.nii.gz
Oliver 44.0 M Oliver2019_09_15/dir_D99.nii.gz
Oliver 47.0 M Oliver2019_12_08/dir_D99.nii.gz
Oliver 50.0 M Oliver2020_03_14/dir_D99.nii.gz
Oliver 53.0 M Oliver2020_06_10/dir_D99.nii.gz
Oliver 56.0 M Oliver2020_09_18/dir_D99.nii.gz
Oliver 59.0 M Oliver2020_12_18/dir_D99.nii.gz
Pickle 38.0 M Pic
by
Doughboys
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AFNI Message Board
Hello Gang,
I was running a 3dLME command:
3dLME -prefix 3dLME_glt.nii.gz -jobs 20 -mask template2_mask2mm.nii.gz -model "Sexe*age" -qVars "age" -ranEff "~1+age" -num_glt 4 -gltLabel 1 "05MF" -gltCode 1 "Sexe : 0.5*M +0.5*F age :" -gltLabel 2 "1MF" -gltCode 2 "Sexe : 1*M -1*F age :" -gltLabel 3 "1MF" -gltCode 3 &
by
Doughboys
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AFNI Message Board
Actually, obliquity seems to be purged with 3dAllineate too...
Anyway, the way to fix it might be to do:
3dWarp -deoblique -prefix ANAT_DEOB.nii.gz
3dWarp -deoblique -prefix EPI_DEOB.nii.gz
I will have the bold and others images a little bit blurred, but I don't see another option...
At least it will fix the obliquity problem for all the other images (T2, DTI) etc.. that need t
by
Doughboys
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AFNI Message Board
I also tested @animal_warper directly on the anatomical image, without 3dCM or deoblique.
I think I might have figured out why the result might have been confusing for some people.
basically, if you run @animal_warper on a T1 with obliquity, @animal_warper will register the image to the T1 with the obliquity purged?
Clem
by
Doughboys
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AFNI Message Board
hello pt
I pushed a little bit my analysis
1. I confirm that the remaining differences of brain orientations using 3dCM (between anat and bold) create misalignment when using afni_proc.py in a second time.
2. I tried to not deboblique the anat and to just use 3dCM prior to @animal_warper. This was a huge fail since I realize that 3dCM and @Align_Centers are actually doing deboblique by defa
by
Doughboys
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AFNI Message Board
thank you pt,
If I understand correctly, 3dCM will still create some minor misalignment on the anat and on the BOLD due to the differences in the calculation of the center of mass (mask for fMRI, without or with a different mask for the anat).
I have done something similar to what you proposed and these little misregistrations had impacted somehow the precision of fMRI co-registration (I have
by
Doughboys
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AFNI Message Board
thank you for your answer!
What do you think is my best options here?
-Recenter the brain to (x, y, z) = (0,0,0) and then -deoblique?
-Abandon deoblique, it is creating more problems than it solves?
-Something else?
by
Doughboys
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AFNI Message Board
Thank you pt,
I have run your command,
they do align perfectly =(
I can send you a few examples if you want, no problem
Do you prefer a link or do you need to send me a repository link? How many images do you need?
by
Doughboys
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AFNI Message Board
Sorry, to come back to you,
The all co-registration process just ended for all monkeys
it seems that the command
3dcopy DSET_ORIG tmp
3drefit -oblique_recenter tmp+orig
3drefit -deoblique tmp+orig
3dcopy tmp+orig DSET_NEW
works for some of the data but creat misregistration for others by not aligning correctly "DSET_NEW" functional image and "DSET_NEW" anatomic
by
Doughboys
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AFNI Message Board
Hello Paul,
I have a new question, sry,
suppose that I need to reverse the command
3dcopy DSET_ORIG tmp
3drefit -oblique_recenter tmp+orig
3drefit -deoblique tmp+orig
3dcopy tmp+orig DSET_NEW
in order to send an atlas in DSET_NEW space back to ORIG space (DSET_NEW to DSET_ORIG space).
Basically reversing the deoblique and oblique_recenter
What would be the command?
Than
by
Doughboys
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AFNI Message Board
Sure, to make it simple
if modify the center of a functional image with
@Align_Centers -overwrite -base dset_anat_deob -dset dset_bold_deob -prefix BOLD_rs_tshift_deob_RECEN.nii.gz -shift_xform_inv Anat_rs_tshift_deob_RECEN.1D
this is not going to create regrinding issues? since I am just translating the center of the image?
by
Doughboys
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AFNI Message Board
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