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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rick reynolds
May 09, 2022 01:57PM
Hi Philipp,

Sure, please send me the "Details" files via email (click on my name), and I will take a look. It is actually a little odd to see a missing slice error for Siemens mosaic files, which makes me wonder if there are multiple acquisitions in that set of 7590 inputs.


For the second question, -assume_dicom_mosaic should not affect the computation of the center. One option would be to add -use_obl_origin.

If you were to run a test with "3dWarp -deoblique" on both the anat and EPI (to resample onto a cardinal grid while preserving the coordinates implied by the oblique matrix), they should overlap reasonably well (depending on how much the subject moved in the mean time).

Of course, the coordinates given by the message are so close, you will not even be able to tell with this particular subject. :)

- rick
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Subject Author Posted

Dimon – "Error: missing slice(s) in first volume!"

Philipp May 06, 2022 04:26AM

Re: Dimon – "Error: missing slice(s) in first volume!"

rick reynolds May 09, 2022 01:57PM

Re: Dimon – "Error: missing slice(s) in first volume!"

rick reynolds May 09, 2022 02:47PM

Re: Dimon – "Error: missing slice(s) in first volume!"

Philipp May 11, 2022 02:11AM