AFNI Message Board

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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June 17, 2019 12:29PM
Dear afni experts.
I acquired a functional data that only covers the posterior part of the brain (see attached). I found it is very hard to align it to a T1 volume. I have several questions here:

1. I tried the method here, but it did not work very well.
2. Is there any method that I can use such that I can first manually align it (I typically use itksnap or the Nudge plugin in afni), then ask align_epi_anat to fine tune it? I find that align_epi_anat has the '-pre_matrix' option which seems can achieve that. But I tried it also did not work very well.
3. I also acquired a high-resolution T2 volume. Not sure whether it can help. I am thinking of aligning T2 to T2 and then epi to T2...

Any suggestion here?

ruyuan
Attachments:
open | download - Screen Shot 2019-06-17 at 10.21.22 AM.png (258.7 KB)
Subject Author Posted

partial coverage alignment Attachments

ruyuanzhang June 17, 2019 12:29PM

Re: partial coverage alignment

ptaylor June 17, 2019 01:33PM

Re: partial coverage alignment

ruyuanzhang June 17, 2019 03:07PM

Re: partial coverage alignment

ptaylor June 17, 2019 07:39PM

Re: partial coverage alignment

Peter Molfese June 20, 2019 05:11PM

Re: partial coverage alignment

ruyuanzhang June 21, 2019 01:29PM

Re: partial coverage alignment

ptaylor June 21, 2019 01:51PM

Re: partial coverage alignment

Peter Molfese June 21, 2019 02:05PM

Re: partial coverage alignment

ruyuanzhang June 21, 2019 03:11PM

Re: partial coverage alignment

ruyuanzhang June 27, 2019 03:40PM

Re: partial coverage alignment

Peter Molfese June 27, 2019 04:07PM

Re: partial coverage alignment

ruyuanzhang June 27, 2019 04:57PM

Re: partial coverage alignment

Peter Molfese July 01, 2019 10:20AM

Re: partial coverage alignment

ruyuanzhang July 08, 2019 03:36PM

Re: partial coverage alignment

paul.hamilton July 03, 2019 03:40PM

Re: partial coverage alignment

Peter Molfese July 04, 2019 10:29AM

Re: partial coverage alignment

paul.hamilton July 13, 2019 08:27AM

Re: partial coverage alignment

Peter Molfese July 15, 2019 02:42PM

Re: partial coverage alignment

paul.hamilton July 17, 2019 11:31AM

Re: partial coverage alignment

Peter Molfese July 18, 2019 03:47PM

Re: partial coverage alignment

paul.hamilton July 23, 2019 09:34AM

Re: partial coverage alignment

paul.hamilton July 23, 2019 10:31AM

Re: partial coverage alignment

Peter Molfese July 23, 2019 10:46AM

Re: partial coverage alignment

paul.hamilton July 24, 2019 03:39PM

Re: partial coverage alignment Attachments

paul.hamilton August 05, 2019 09:10AM