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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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I am the same problem.
Can you explain better the whereami function?
When I ask: whereami -show_available_spaces TLRC, the answer is:
++ ----- List of available spaces: -------
++ TT_N27
++ TT_avg
++ MNI
++ MNI_ANAT
++ MNIa
++ MNI_SPM2
++ MNI_FSL
++ MNI_OTHER
++ HaskinsPeds
However, if I try:
whereami -mask_atlas_region TT_Daemon:right:putamen -prefix Putamen_right -space MNI
by
Emmanuelle Renauld
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AFNI Message Board
Hi AFNI experts,
When I use 3fim+ for the seed-based analysis, I often see many zeros (many small "holes" in the final correlation map). I had always thought that they were real zeros. But I just noticed that sometimes, it happens even very close to the seed, (and all neighboring voxels are close to 1, as they should).
This is my command line (mask_ideal is created with 3dmaskave
by
Emmanuelle Renauld
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AFNI Message Board
Hi,
thank you for your quick answer.
>> Concerning Fisher transforms. AFNI proposed that we do it before running seed-based analysis.
> No, that's not true. Fisher transformation is typically performed after the seed-based correlation analysis at the individual level, but before group analysis. Such practice is typically adopted in the whole neuroimaging community.
Yes,
by
Emmanuelle Renauld
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AFNI Message Board
Hi,
Concerning Fisher transforms. AFNI proposed that we do it before running seed-based analysis. Why is it so important to have Gaussianity for seed-based analysis?
I have come upon some situations where I think it creates false results. Under the seed, the correlation coefficients should be really high, because the seed should be well connected with itself. Let's say ~1. However, af
by
Emmanuelle Renauld
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AFNI Message Board
Super, thank you!
I ran @Align_Centers on both anat and epi (to pre-align them on MNI) and I re-ran everything and this time it worked much faster.
Once again, this forum saves my life!
by
Emmanuelle Renauld
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AFNI Message Board
Hi Bob,
I tried as you said (with my own program since I am working in bash). Even with as few as 5 TR, it still gets killed.
I also tried with autobox first to try to reduce the size of the EPI. Result was ++ Auto bbox: x=16..60 y=5..65 z=0..33
Result of the 3dNwarpApply was
++ 3dNwarpApply: AFNI version=AFNI_16.3.08 (Nov 4 2016) [64-bit]
++ Authored by: Zhark the Warped
++ opene
by
Emmanuelle Renauld
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AFNI Message Board
Hi again Bob and other AFNI experts,
to continue with this story, I applied 3dNwarpApply as discusted on a first set of data, everything went well. Now I have a new one, and the script keeps getting "killed". My guess is that it is because there is not enough RAM. The same issue was presented here but my data are not so far apart so I don't think that's the problem. I als
by
Emmanuelle Renauld
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AFNI Message Board
Thank you very much for your answer, I will indeed invert my other matrices first.
I just started preparing my script for the nonlinear registration, I look forward to seeing the results!
by
Emmanuelle Renauld
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AFNI Message Board
Hi AFNI members,
I wanted to concatenate my matrices from the volume registration, epi2anat (I have anat2epi that I inverse), and anat2tlrc (I have MNI to anat that I inverse).
When I was using linear registration for the anat to tlrc, I had this line:
>> cat_matvec -ONELINE -I -I volreg_matrix.aff12.1D > whole_matrix_volreg_epi2anat_tlrc.aff12.1D
Now I am trying to do
by
Emmanuelle Renauld
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AFNI Message Board
Hi,
I know that this is an old topic, but I'm a little lost with all the answers.
I want to do nearly the same: I prefer Freesurfer's skullstripping. But in their pipeline, they modify (they "conform") the shape of the raw T1 to make it 256x256x256. They also seem to deoblique the data.
Then, I use @auto_tlrc to register the skullstripped T1 to MNI. But the result
by
Emmanuelle Renauld
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AFNI Message Board