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

History of AFNI updates  

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Daniel Glen
October 31, 2008 12:02PM
You can view the slice timing with

3dAttribute TAXIS_OFFSETS dset+orig

Slice timing can be corrected with an alternate time pattern than the one stored in the header with
3dTshift -tpattern ... dset+orig

where the tpattern option can be specified per the help for 3dTshift
-tpattern ttt = use 'ttt' as the slice time pattern, rather
than the pattern in the input dataset header;
'ttt' can have any of the values that would
go in the 'tpattern' input to to3d, described below:

alt+z = altplus = alternating in the plus direction
alt+z2 = alternating, starting at slice #1 instead of #0
alt-z = altminus = alternating in the minus direction
alt-z2 = alternating, starting at slice #nz-2 instead of #nz-1
seq+z = seqplus = sequential in the plus direction
seq-z = seqminus = sequential in the minus direction
@filename = read temporal offsets from 'filename'

Alternatively, you can reset the attribute in the header with 3drefit

3drefit -atrfloat TAXIS_OFFSETS "..." dset+orig

with the correct time offsets inside the quotes following "TAXIS_OFFSETS"

One other way is to reread the .BRIK file or original DICOM files with to3d and specify the correct tpattern and all the other specifications for the data.
Subject Author Posted

slice timing in BRIK header

Young October 31, 2008 11:47AM

Re: slice timing in BRIK header

Daniel Glen October 31, 2008 12:02PM

Re: slice timing in BRIK header

Daniel Glen October 31, 2008 12:07PM

Re: slice timing in BRIK header

Young October 31, 2008 12:58PM

Re: slice timing in BRIK header

Daniel Glen October 31, 2008 01:20PM

Re: slice timing in BRIK header

Young October 31, 2008 01:28PM

Re: slice timing in BRIK header

Daniel Glen October 31, 2008 02:12PM

Re: slice timing in BRIK header

rick reynolds October 31, 2008 02:21PM

Re: slice timing in BRIK header

rick reynolds March 11, 2013 03:49PM