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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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Hello,
I encountered the same problem. Have you figured out how to tell afni that this is a 3d data?
Thanks!
by
Meizhen
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AFNI Message Board
Hello,
I had one condition in one run, two conditions in two runs, but I wanted to do contrast between the two runs, one condition minus the other condition. I tried 3dbucket to bucket the two epi together, and 3drefit the TR. But something went wrong doing glt. It had time files, but the stim_times were guessed and using GLOBAL times? I could not figure out why and how could I do the contras
by
Meizhen
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AFNI Message Board
Hi Daniel,
I used the resize tricky to do the skull-stripe, it looks nice, but when I check the alignment, I found that the brain size in epi and structure images were not the same. I resized the 0.5mm isotropic structure images to 1mm isotropic and 1mm isotropic original epi images to 2mm isotropic. What went wrong?
Thanks for your patience and kind help.
Meizhen
by
Meizhen
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AFNI Message Board
Sorry, I should pointed it out. The files are available for download at www.cerebralsystems.ca.
Thanks,
Meizhen
by
Meizhen
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AFNI Message Board
Hi Daniel,
Actually I found a catlas publicly available:
Catlas: An magnetic resonance imaging‐based three‐dimensional cortical atlas and tissue probability maps for the domestic cat (Felis catus)
But I don't know how to combine it into afni as a 'standard' template for tlrc Can you help me?
Thanks,
Meizhen
by
Meizhen
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AFNI Message Board
Hi Phil,
Thanks very much, yes, I set it RPI and it worked!
Meizhen
by
Meizhen
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AFNI Message Board
Hi Daniel,
Thanks very much for your information. It's helpful. I tried and it turned out to be much better!
Thanks,
Meizhen
by
Meizhen
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AFNI Message Board
Hi Rick,
Thanks for your reply, I was new to this forum at that time, and I missed your reply... I've already figured it out by doing 3drefit.
Thanks.
Meizhen
by
Meizhen
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AFNI Message Board
Hi Daniel,
Thanks for your information. That's very nice of you.
Actually I tried doing skull stripe on monkey template, with fc from 0.1-0.2, it could run with single 3dSkullStripe, but it failed in align_epi_anat.py -anat2epi, for it could not do skullstripe in align's default option. My purpose is to do resting connectivity analysis, now got stuck in this step.
Thanks.
Meizhe
by
Meizhen
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AFNI Message Board
Hello,
I am trying to do skull stripe on cat's brain. But there is no cats' template, do you have some suggestions on by doing it on afni. I tried to modify the parameters on monkey's template, but it didn't work well.
Thanks.
Meizhen
by
Meizhen
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AFNI Message Board
Hi, sir,
I am new in afni using, can use afni proc.py analyze single shot epi data. But has problem in applying it to analyze multishot . The main problem is the TR correction and stim time mapping in the timecourse.
Best regards,
Meizhen
by
Meizhen
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AFNI Message Board