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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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Dear AFNI,
I have fMRI data acquired with an interleaved slice selection in the sagittal plane instead of axial. I want to do slice timing correction with 3dTshift. Do I need to permute the X and Z axes before 3dTshift, or does AFNI just "know" what the correct slices are and how to correct them?
thanks,
Michael
by
michael tobia
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AFNI Message Board
...just to expand on this...
the CENSORTR specifically is not working correctly, and it is censoring the first 2 volumes, setting them to ZERO if that is the -cenmode. However, the -censor flag seems to work correctly.
~michael
by
michael tobia
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AFNI Message Board
Dear Afni,
I'm using 3dTproject to orthogonalize motion and bandpass filter some resting state time series. I have the -CENSORTR option turned on, but it seems to not be working correctly, at least for some data sets. The problem is that in some cases the CENSORTR file that I specify does not contain any volumes to censor, but 3dTproject reports that it has in fact censored a few volume
by
michael tobia
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AFNI Message Board
Nice catch! R was not installed on this machine (but the error messge was the same as your website, which left me thinking it was a problem with the builds). Just installed it and the help files are working properly now.
Thanks!
~mike
by
michael tobia
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AFNI Message Board
Hi Rick,
Thaks for fixing the web help.
Yeah, my latest afni update produces 'R: command not found' when I use 3dMVM -help.
~mike
by
michael tobia
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AFNI Message Board
Dear Afni,
I recently updated my afni and noticed that help files for programs that use R (i.e., 3dLME or 3dPFM, etc) are missing. Also, the help files for these programs are not on the website either. Will there be continued support for these programs, and can you please replace the help files for the versions that already exist?
thanks,
mike
by
michael tobia
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AFNI Message Board
Hi Rick,
Thanks again, I really appreciate your insights. I guess the question about 'how can 3dvolreg detect such small motion?' implied the part about it being reliable. Perhaps the original question should have been 'how can 3dvolreg reliably detect small motions?' Regardless, I was assuming that vibrations from the scanner itself could cause these motions in our phan
by
michael tobia
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AFNI Message Board
Hi Rick,
Thanks for the explanantion. As long as these micromovements are reliably detectable by 3dvolreg, then I'm satisfied.
cheers,
michael
by
michael tobia
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AFNI Message Board
Hi Rick,
These miniscule/small movements are not a problem at all. I'm just curious how 3dvolreg finds them when the grid is 2.5 x 2.5 x 2.5. Does it only use the edges of the phantom, or does it make use of the "structural" information (there are wires inside it) inside the phantom as well when performing the registration? If it uses structural information inside the phantom
by
michael tobia
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AFNI Message Board
Dear Afni Experts,
What is the minimal amount of motion that 3dvolreg can detect and output in the motion params? I have a spherical water phantom that obviously cannot move much, but I 3dvolreg-ed it anyway and when I looked at the motion params it finds rotations and translations in each that are much, much smaller than the voxel size. For example, movement of .01 degrees in the yaw, or .0
by
michael tobia
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AFNI Message Board
Hi Daniel,
Thanks for this suggestion - I think scaling in the 3dcalc will increase the "intensity" of the rgb image.
cheers,
michael
by
michael tobia
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AFNI Message Board
Hi Guys,
Thanks for quick replies. This is what I was asking for, but it did not fully solve my problem. My RGB image is very dark for some reason, and even on the white background it appears mostly blackish. I can see some red, green and blueish hues, but the image is fully opaque, even though I used the -fim flag for 3dThreetoRGB. Is there a way to rescale the RGB to have better brightne
by
michael tobia
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AFNI Message Board
Dear Afni experts,
Is it possible to change the image viewer display to have a white background color instead of black? I'm trying to view an RGB map and it appears very dark and almost invisible on the black backcolor. I tried loading it as a volume in SUMA where I can toggle the backcolor from black/white, but it crashed the program. Any suggestions?
thanks in advance,
michael
by
michael tobia
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AFNI Message Board
Dear Ziad and Nick,
Thanks for the suggestions. I'll give Nick's solution a try this week and let you know how it worked. Also, I uploaded some data for you to the AFNI server with the folders and files you requested.
thanks for your help!
Michael
by
michael tobia
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AFNI Message Board
Dear Ziad and Afni Experts,
I'm trying to compare cortical thickness for the affected hemisphere of a patient group to their unaffected hemisphere (the affected hemisphere is sometimes left and sometimes right, so it requires surface node/vertex symmetery). Is it possible to use SUMA_Make_Spec_FS to generate a SUMA surface from the lh.rh.sphere.reg (it's the output from freesurfer
by
michael tobia
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AFNI Message Board
Dear Afni,
I'm trying to use @toMNI_Awarp in prep for @toMNI_Qwarpar, but I get the following error:
***** @toMNI_Awarp: Failed to find template MNI152_1mm_uni+tlrc -- cannot continue
I checked my abin folder and I don't have this MNI152_1mm_uni+tlrc template file in it. Where can I get it, or how can i resolve this error?
thanks,
michael
by
michael tobia
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AFNI Message Board