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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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That did the trick (see attached)!
Many thanks for both of you for your help!
Bests,
Philipp
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philippn
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AFNI Message Board
Thank you very much for the link, Sam and Paul for your comments!
I tried methods 4 and 5, as I have an image without noise for masking and the normalization after @SSwarper looks fine!
For some reason, however, does the skullstripped anatSS image not match the original anat anymore? See attached image.
Do you have an idea of what happened?
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi Paul,
thanks for your response! I think you are right, as there are also 3 other types of structural images that have been recorded (cf. file attached). Unfortunately, I don't know how these images are being combined.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi all,
I am facing a challenge with processing T1w images that have a noisy background making it difficult to process them with 3dSkullStrip and @SSwarper (see image attached). Do you have any idea how to tackle this problem?
Happy to provide an example nifti.
Thanks and bests,
Philipp
by
philippn
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AFNI Message Board
Hi Peter and Daniel,
thank you for your helpful suggestions!
Based on your feedback, I finally managed to successfully coregister the b0 image to the hires space via the anat using the align_eip_anat.py, 3dQwarp and 3dNwarpApply commands (cf. attached image top 2 rows vs bottom 3 rows).
For some reason I was under the impression that you have to go through MNI space, which very much compl
by
philippn
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AFNI Message Board
Hi, I am bringing up my problem described above again, since it still persists.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi all,
I want to coregister an averaged DWI b0 image (left side in attachment) to a high-resolution image slab, that only covers the brainstem (right side in attachment) within subject. I unsuccessfully tried a combination of align_epi_anat and 3dresample.
E.g.
1.
align_epi_anat.py -overwrite -dset1 hires+orig. -dset2 anat+orig. -dset1to2 -dset1_strip None -edge -cost lpa
align_epi_anat.p
by
philippn
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AFNI Message Board
Hi,
I sent you an email with the requested information last Thursday.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi Rick,
thank you for your help with the shell error messages! I fixed them and they are gone whenever I start them. The main issue with the error "set: Variable name must begin with a letter." unfortunately still persists when using @SUMA_AligntoExperiment. (see attachment)
May I send you my current dotfiles again per email just to make sure that there is nothing wrong here?
by
philippn
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AFNI Message Board
Hi Rick,
the same error now occurred also to me hence I am reviving this old thread.
I am running afni on a Macbook Pro 14 with Macintosh 12 Monterey.
afni -ver gives:
Precompiled binary macos_10.12_local: Mar 10 2022 (Version AFNI_22.0.17 'Hadrian')
I send you the other output via PM.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi,
"Well, I guess I asked for it... Silly me."
I am still happy that you did :) The procedure turns out to be far more complex than I expected.
"In the transformation_steps.jpg image you sent, is Panel A-left really a subject native space thing? It looks like a template."
You are right, the left image in rows A and B is the MNI152_T1_1mm.nii.gz template. The respecti
by
philippn
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AFNI Message Board
Hi,
I would like to discuss options for nonlinear processing and opened another thread called "Nonlinear registration for hires slab" with more detailed information about my idea and data.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi all,
as promised in my last thread "3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file " and encouraged by ptaylor :) I would be happy to discuss nonlinear registration of my data set. As you can see from the attached image "ROI_alignment_comp" the affine transformation was not successful - the red circle (m
by
philippn
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AFNI Message Board
Thank you for your answer and the background information.
I'll watch these videos. After taking a closer look at the registration, the anat-->MNI transformation underperforms quite a bit using 3dAllineate. I may switch to 3dQwarp and 3dNwarpApply to see whether this improves things. I would open a new thread though as this topic has been dealt with successfully :)
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi,
thanks again for your patience and thorough support! In the end it turned out there was a typo in the cat_matvec command. It works now and the transformed atlas ROI looks beautiful in native space :)
"And I ran:
align_epi_anat.py \
-dset1 short_epi+orig. \
-dset2 FT_anat+orig. \
-dset1to2 \
-partial_axial \
-dset1_strip None \
-dset2_strip None \
by
philippn
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AFNI Message Board
Hi rick and ptaylor,
thank you very much for your valuable input! I can follow the idea of having eventually a "stack" of transformation matrices that can be used to warp an atlas ROI in MNI space via an anatomical image to EPI (native) space. Regarding the registration between an anatomical and a template brain I was satisfied with running @SUMA_AlignToExperiment and using the follo
by
philippn
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AFNI Message Board
Hi Rick,
thanks for your fast response!
I followed your advice and called 3dAllineate with the following command:
3dAllineate -prefix ROI_in_native_space -base native_image.nii -source atlas_ROI.nii -twopass -cost lpa -1Dmatrix_apply native_al_mat.aff12.1D -autoweight -cmass -twobest MAX
The good news is that the program worked. The bad news is that the ROI is far off from where it sh
by
philippn
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AFNI Message Board
Hi all,
I want to warp ROIs from an atlas to a native image space, which only consists of several slices covering the upper part of the brainstem. To this end, I aligned the native image to a native structural image using align_epi_anat.py resulting in a native_al+orig and a native_al_mat.aff12.1D file .
Next, I aligned the atlas space MNI template image to the structural image using @SUMA_Al
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philippn
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AFNI Message Board
Hi Gang,
does this mean in my case I don't have happy/sad but time1/time2? Otherwise I don't understand how my WS factor time is accounted for in addition to the condition.
Bests,
Philipp
by
philippn
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AFNI Message Board
Hi all,
I want to do a paired t-test using 3DMEMA for a dataset where each participant was scanned twice (t1, t2). I modeled the data with 3dDeconvolve separately for each participant and each session. In the 3dMEMA example for paired t-tests it seems to me like there is only one beta-coef (B+tlrc) and one t-stat (T+tlrc) BRIK necessary for each subject and contrast:
Example 3 --- Paired ty
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philippn
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AFNI Message Board