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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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Awesome! I'll then detrend it using the 3dTproject.
Thank you so much as always!
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irenej24
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AFNI Message Board
Hello —
It's my first time working on the resting state data, and I would like to ask about which file to use as the ort input.
To note this first, I'm not using afni_proc.py (sorry!) and using the output from fmriprep and have deobliqued and blurred the data as a preprocessing step.
I put my motion parameters in a 1D file where each column has each parameter's info, which I
by
irenej24
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AFNI Message Board
Oh, but visually, they look really well aligned even though the obliquity isn't the same (attached the pictures)!
Do you think it is still not cool to use it as it is as they don't have the same obliquity?
by
irenej24
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AFNI Message Board
Thank you so much!
Yes, the output of @SUMA_AlignToExperiment now has the same grid as the input T1, but the obliquity is different. My anatomical T1 input had obliquity. and the output doesn't have any (just like the SurfVol file).
Do you recommend deobliquing the data (T1) from the beginning (before doing @suma_make_spec_fs)? I have other functionally defined ROIs from the obliqued d
by
irenej24
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AFNI Message Board
I would like to use Freesurfer aseg atlas (aparc.a2009_aseg.nii) in the subject space. I think I'm so close and I found other posts related to this, but I can't still figure out how to get the atlas in the native space.
I ran @SUMA_Make_Spec_FS (command I ran: @SUMA_Make_Spec_Fs -NIFTI -sid sub-01), and it created the SUMA directory, which has subj_SurfVol.nii and aparc.a2009s+aseg.n
by
irenej24
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AFNI Message Board
Hi Daniel,
Could I ask one more thing?
I've decided to twig the color of gray02 map. So, I used MakeColorMap, with a text file containing ;
#i Label R G B A
1 bright 0.35 0.35 0.35 1
2 dark 0.6 0.6 0.6 1
(MakeColorMap -usercolutfile - MyTextFile.txt - suma_cmap gray20)
Then, there comes three colors, and when I check it with 'MakeColorMap -std gray02', it
by
irenej24
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AFNI Message Board
Thank you so much, Paul and Daniel!
I think I got the idea how to play with different color/contrast ranges.
Have a lovely day! :)
by
irenej24
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AFNI Message Board
Hi all,
I have a quick question about adjusting color/contrast of underlay brain in SUMA.
I'm using 'grey02' colormap, but want to have it with less contrast so that the actual data can be more salient. I found that I can adjust 'dim' in Surface Controller, but is there any other way to just change the color or contrast of an existing colormap?
Thank you in advance
by
irenej24
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AFNI Message Board