Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 12 of 12
In the beginning I was confused was the best method to apply and I had different comments and any of them was really clear. I have to say this is my first fmri data I am analyzing, I checked the boot-camps and reading I am convinced that both are reliable. Now I am using MACAQUE_DEMO_REST as guideline. Sorry if my question was not clear and very basic.
Thanks
Fabian
by
Fabian
-
AFNI Message Board
Hi everyone,
I have a question: I have fmri data. I am using the tutorial in the in macaque demo and works perfect. I have this kind of data.
T1w - fieldmapAP - fieldmapPA - fmriAP(15min)- fmriPA(15 min)
The first part T1w aligment to the NMT2 no problem (@animal_warper)
However, I am not clear how to use epi_b0_correct, because in the demo afni_proc.py, uses only one epi, but it is the orig
by
Fabian
-
AFNI Message Board
Hi Taylor,
The T1w from the current mri. I did before
3drefit -deoblique -orient LSP T1w.nii.gz
Because the orientation is like the image you see at the end.
Horizontal - Sagittal - Coronal view from afni.
If I applied 3drefit -deoblique -orient LSP then the orientation is agreed with the view in afni
I applied to the original mri
3dWarp -deoblique -disp_obl_xform_only DSET_NAME
out
by
Fabian
-
AFNI Message Board
Hi Taylor,
Probable my statement "not perfect coronal cut" is incorrect. I attached first the 2011 mri I can see the chamber perpendicular and the second 2020 the same chamber but in angle and checking this mri I don't see the chamber correctly in the coronal view.
3dinfo -orient -obliquity T1w.nii.gz
output
LSP 0.000
Looking now the two mri the sagittal is not proper po
by
Fabian
-
AFNI Message Board
Hi Afni experts,
I have a question, we did a anatomical mri to macaque, but the orientation looks not perfect coronal cut, and by extension in all the others planes. How I know, because I have a previous mri from several years back and the image are not similar, and from the horizontal view the hemispheres are very asymmetrical
I would like to reoriented the mri and reslices coronal view. I tr
by
Fabian
-
AFNI Message Board
Hi Taylor,
I did this
3dZeropad \
-I -80 \
-S -40 \
-prefix T1w_recent_crop.nii.gz \
T1w_recent.nii.gz
I repeated the alignment we did before, no problem
I downloaded the NMTv2 and I did
@animal_warper -input T1w_recent_crop.nii.gz \
-base ~/Documents/Software/NMT-master/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm.nii.gz \
-atlas
by
Fabian
-
AFNI Message Board
Hi Taylor,
Thanks for the all the advice. I started to see the anfi bootcamp.
I run the command and the script again and looks more better, I see the coronal is not complete overlay. Is there a procedure to improve it?
Other question, you mention that it would be better if I crop the mri to extract the brain. Is there a method to do with afni or is possible to do with matlab and write as nifti
by
Fabian
-
AFNI Message Board
Hi Taylor,
First, this is the code I used:
@animal_warper -input T1.nii.gz -base /home/maestro/Documents/Software/NMT-master/NMT_v1.2/NMT.nii.gz -atlas /home/maestro/Documents/Software/NMT-master/NMT_v1.2/atlases/D99_atlas/D99_atlas_1.2a_al2NMT.nii.gz
the output of 3dWarp -deoblique -disp_obl_xform_only T1.nii.gz
++ 3dWarp: AFNI version=AFNI_20.2.14 (Aug 21 2020) [64-bit]
++ A
by
Fabian
-
AFNI Message Board
Hi Taylor,
Yes, the monkeys are in sphinx position and I figured out when I checked them by using afni:
I attach the afni display for the T1.nii.gz
First row, it is the original structural MRI
Second row after applying 3drefit -orient RIP T1.nii.gz
and I applied for both the @animal_warper I have the same distortion and unsuccessful in the template overlay
output afni -version : Precompile
by
Fabian
-
AFNI Message Board
Hi Everyone,
I am new using afni and the all the suit. To the point, I have several NHP MRIs but in particular I am interesting to do reconstruction of recording sites by electrophysiology. I applied the @animal_warper to the example_subject no problem everything was ok, when I applied to my MRIs was totally distorted (I tested with 2 MRI). Check with detail I figured out that the order (sagitta
by
Fabian
-
AFNI Message Board