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

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AjaySK
November 18, 2014 01:13PM
Hello Afni Experts,
I had a question regarding the pipeline as I also had data that I preprocessed on my own.

1) My EPI images are in RPI orientation so is it necessary to run 3daxialize/3drefit -deoblique? The images were taken at an oblique angle but I have all of my masks/anatomicals already aligned to the EPI and so is this necessary? If it is necessary, since my images are in RPI orientation could I get away with just 3drefit -deoblique?

2) Does 3dZcat at later stages only work with images that are deobliqued for stacking in the z direction or would it work if all three TE's have the same oblique angle and aligned to the same reference scan?

3)If I have multi-echo data that is desike, tshift, volreg,filter (highpass 0.005 to 99999), and smoothed (5mm 3dBlurtoFWHM) for each TE, is it possible to input this file into meica.py for the ica analysis in native space without redoing the preprocessing? I can disable some options but I wasnt sure if I can disable tshift.

Thanks,
Ajay
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Subject Author Posted

Multi echo ICA question

jk619 July 30, 2014 10:00AM

Re: Multi echo ICA question

kundup July 30, 2014 01:03PM

Re: Multi echo ICA question

jk619 July 31, 2014 05:58AM

Re: Multi echo ICA question

kundup August 01, 2014 11:40AM

Re: Multi echo ICA question

jk619 August 04, 2014 06:34AM

Re: Multi echo ICA question

jk619 August 13, 2014 08:52AM

Re: Multi echo ICA question

AjaySK November 18, 2014 01:13PM