Hi,
it is also important to keep in mind that, depending on the multiband factor, multiple slices are acquired at the same time, so just entering the exact order into a standard slicetiming algorithm won’t give you the right results. Usually slice times are calculated using the slice order and TR but that will not work for multiband as multiple slices have the same acquisition time. I can not tell you though if there is an option in FSL to enter the exact slice times instead of just order and TR.
Cheers,
Norman
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Dipl.-Inf. Norman Scheel
UNIVERSITÄT ZU LÜBECK, Germany
KLINIK FÜR NEUROLOGIE
MGZ Lübeck, 2. OG
Paul-Ehrlich-Straße 1-3
23562 Lübeck
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Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Harms, Michael
Gesendet: Donnerstag, 12. Februar 2015 16:24
An: [log in to unmask]
Betreff: Re: [FSL] How to obtain correct slice acquisition order of multi-band rsfMRI acquisition ?
Hi,
I don't know if I would trust any of the DICOM general time stamps to have that degree of accuracy. There is a field in the Siemens private vendor fields called "MosaicRefAcqTimes" that contains the relative slice timing info for that particular acquisition to within a 2.5 ms interval. You can easily find this info by running a DICOM through the 'strings' command, and locating that text string. Probably best to do this with the 2nd or later DICOM, because for a while, there was a bug in the multiband sequence such that the info wasn't accurate for the 1st DICOM in a timeseries.
cheers,
-MH
--
Michael Harms, Ph.D.
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Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
From: Michael Knight <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, February 11, 2015 9:58 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] How to obtain correct slice acquisition order of multi-band rsfMRI acquisition ?
I believe it uses Siemens even interleaved, i.e. slice groups [2 4 6 ...] then [1 3 5...], where "slice group" is a set of simultaneously acquired slices. Chris Rorden's dcm2nii seems to get the slice timing correct (if you want to convert to .nii.gz). This information is output to the terminal at the time of running dcm2nii, given the time of acquisition of each slice AFTER multiband delineation, otherwise use the dicom time stamp - Matlab's dicominfo command (amongst many others) can get it.
Hope that is of some use
Michael
On 11 February 2015 at 15:27, Paul Chou <[log in to unmask]> wrote:
Dear all FSL experts :
Currently we install the multi band EPI sequence (https://www.cmrr.umn.edu/multiband/) in our 3T Siemens Trio machine . In order to perform slice timing correction for these dataset, I will some of you could teach me how to obtain the correct slice acquisition order of multi-band rsfMRI dataset.
Best and hear feedback from you
Paul
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