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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ejw
June 29, 2015 06:11PM
I have some subject level FSL data (parameter estimate NIFTI files) that I would like to convert/transform into TLRC (TT_N27) space so that I can compare these FSL data with other data generated through AFNI.

I have followed these steps:

1) Deoblique the FSL pe#.nii.gz files using 3dWarp with the -deoblique flag.
2) Generate tlrc space using 3drefit -view
3) Align to standard brain using @Align_Centers -base /home/ghindy/abin/TT_N27+tlrc

To check if this worked, I overlay the transformed and aligned PE file on the anat file generated by AFNI. As is clear from the screenshot, the mask is crooked and too large:

[dl.dropboxusercontent.com]

If I omit the deobliqueing stage (1), the result looks better but still too large:

[dl.dropboxusercontent.com]

If there a better way to get FSL pe.nii.gz files to come into standard TLRC space for comparison to AFNI output?
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Subject Author Posted

Converting FSL output to AFNI

ejw June 29, 2015 06:11PM

Re: Converting FSL output to AFNI

Peter Molfese June 29, 2015 11:30PM