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
November 18, 2012 04:33PM
Gaurav-

Our scanner also does not put the slice timing information into the DICOM and resulting NIFTI files (converted with either dcm2nii or Dimon/to3d). One solution is to add the following line to your afni_proc.py scripts. In our case, the slices are alternating starting at 1 instead of 0 - substitute whatever your slice sequence is for alt+z2. 

-tshift_opts_ts -tpattern alt+z2

Two other options are 1) use nifti_tool to change the slice info (see: [nifti.nimh.nih.gov]). Or 2) use a different DICOM to NIFTI converter, such as dcmstack, which encodes the slice order based on the acquisition time.
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Subject Author Posted

Slice timing correction issue

gauravm November 06, 2012 01:19PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 02:08PM

Re: Slice timing correction issue

gauravm November 06, 2012 03:25PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 03:38PM

Re: Slice timing correction issue

gauravm November 06, 2012 05:13PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 09:48PM

Re: Slice timing correction issue

Daniel Glen November 08, 2012 04:28PM

Re: Slice timing correction issue

gauravm November 18, 2012 04:04PM

Re: Slice timing correction issue

Peter Molfese November 18, 2012 04:33PM

Re: Slice timing correction issue

gauravm November 19, 2012 09:42AM

Re: Slice timing correction issue

rick reynolds November 19, 2012 09:55AM