Hi, One comment: I don’t know about the details of these particular scripts, but users should be aware that different SMS/MB implementations (e.g., CMRR vs. Siemens/MGH) do not necessarily use the same slice ordering. The safest thing to do is confirm the timing from the DICOMs.

cheers, -MH

-- Michael Harms, Ph.D.

----------------------------------------------------------- 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 63110Email: mharms@wustl.edu

On 9/7/16, 4:55 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

On 09/01/2016 04:31 PM, Wang, Ruosi wrote:

Dear Freesurfer developers:

I'm seeking out ways for performing multi-band slice timing correction with freesurfer 5.3. I've searched the mailing list, and noticed that there might be a couple of ways for doing this. But, I still have some conerns for different ways, and please see below for my questions:

1. using new version of stc.fsl and slicedelay

I tried to download these files from a link provided in an emai loop

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg43359.htm l of the mailing archive, but failed to do so. Could you please share the updated downloading link to these files. In addition, what kinds of information shall I provide? The slice order and number of SMS slice groups? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fsl ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fsl ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/slicedelay

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/slicedelay

Try now

2. using freesurfer 6 for preprocessing

Since freesurfer 6 is still in beta version, can I use the proproc-sess of fs6 for data preprocessing only and switch to fs 5.3 afterwards for all the other anlaysis? Is there any downside for this, in comparison with just using the new version of stc.fsl and sliceday?

I would be careful using fs6 for anything you don't want to have to redo.

In addition, for the input file so of -sliceorder, shall it be the slice number ordered by time? And for the input file of -ngroups, shall it be the number of slices that are colloected at the same time?

The slice order is up, down, siemens, etc. The number of groups is the number of slices acquired simultaneously

Thank you so much, it is deeply appreciated. Best, Ruosi -- Ruosi Wang Graduate Student Vision Lab in Psychology Department Harvard University William James Hall, 7 floor 33 Kirkland Street Cambridge, MA 02138

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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