If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30?
Hi Rita, I would not automatically assume that regarding slice ordering with "interleaved" acquisitions, as I don't think that there is necessarily any "standard" that different manufacturers are committed to following. It is actually a non-trivial issue -- e.g., how do scanner choices regarding acquisition mode, image numbering, and direction of graphical slice prescription all relate to each other. You might be able to check with an engineer/technician for your particular platform and confirm how it is done on that platform for your chosen protocol, acquisition parameters, and way of doing slice prescription. But probably easiest to just figure it out empirically by acquiring 4-5 slices (select an even or odd number to match your desired protocol) with a large slice gap and a long TR (e.g., 10 sec), and having the subject rotate his/her head far to the left following the collection of the first slice. The slice acquired first temporally is then easily identified as the non- rotated slice.
cheers, -MH
On Tue, 2011-02-08 at 11:41 -0500, Rita Loiotile wrote:
If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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For Siemens with an even number of slices, it is generally 2,4,6,..30,1,3,...29. This changes if there is an odd number of slices.
doug
Rita Loiotile wrote:
If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For an odd number of slices- e.g. 45- would it just be 1,3,5,...,45,2,4,...,44 for the Siemens default?
On 2/9/11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
For Siemens with an even number of slices, it is generally 2,4,6,..30,1,3,...29. This changes if there is an odd number of slices.
doug
Rita Loiotile wrote:
If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes doug
Rita Loiotile wrote:
For an odd number of slices- e.g. 45- would it just be 1,3,5,...,45,2,4,...,44 for the Siemens default?
On 2/9/11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
For Siemens with an even number of slices, it is generally 2,4,6,..30,1,3,...29. This changes if there is an odd number of slices.
doug
Rita Loiotile wrote:
If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Michael Harms -
Rita Loiotile