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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smoia
September 27, 2022 05:09AM
Hello,

I was testing a couple of options to skullstrip some MP2RAGE data, and I noticed that if I don't deoblique the volume first, 3dSkullStrip changes the Qform and Sform in the header of the file - apparently rounding it up to 1 or down to 0.

See the attached files - the headers (skullstripped volume on the right) and the skullstripped volume (in blue-lightblue) over the original image (the green volume is the result of BET). Note that the voxel offset is also different in the headers.

Is there a way to avoid this behaviour? I am trying to avoid deobliquing the original files, in order to not introduce an extra interpolation in the data. Would overwriting the headers be a good move, or since the change in Qform and Sform happened already, it is too late?

Cheers,
Stefano Moia



Edited 1 time(s). Last edit at 04/03/2023 07:56AM by smoia.
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Subject Author Posted

3dSkullStrip seems to change Sform and Qform of oblique datasets Attachments

smoia September 27, 2022 05:09AM

Re: 3dSkullStrip seem to change Sforma nd Qform of oblique datasets

Daniel Glen September 29, 2022 05:42PM