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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Peter Molfese
June 29, 2015 11:30PM
Is the data already warped to MNI space through the FSL FEAT pipeline? 3drefit doesn't actually do a transformation, it just modifies the file header. Use it only when you believe you know the data should be a particular way (similar to changing the file extension). If you data is in subject space, then you probably want to:

1) Align the anatomical to TLRC using @auto_tlrc
2) Apply that warp to your pe.nii.gz file using @auto_tlrc (usage 2)

If your data was warped to MNI space as part of FSL, then you could try the -mni2tta option of 3dWarp. More information on how you processed your data could be helpful to the debugging process.

Is there a particular reason you're using FSL for this particular data?
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Converting FSL output to AFNI

ejw June 29, 2015 06:11PM

Re: Converting FSL output to AFNI

Peter Molfese June 29, 2015 11:30PM