Sorry for the slow response (at OHBM). Yes, that sounds correct. If you pass it a file, then all other options are ignored.
On 6/12/2019 7:12 AM, Joseph Dien wrote:
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Okay, I looked through the source code itself and I think I worked it out.
preproc-sess calls on stc-sess, passing it both the sdf and the ngroups flags. stc-sess calls on stc.fsl, passing it both the sdf and the ngroups flags. stc.fsl calls on slicetimer. It uses the sdf flag if it has been set to a file name, otherwise it uses the other flags including ngroups to call on slicedelay to generate an sdf file which it then passes on to slicetimer.
So in other words, if an sdf file is provided, then the ngroups flag is ignored and does not need to be set.
Am I correct? I’d like to make sure I’m doing this right.
Thanks again for this amazing toolset!
Joe
On Jun 11, 2019, at 15:55, Joseph Dien <jdien07@mac.commailto:jdien07@mac.com> wrote:
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looking further into the archives, I see that the -sdf flag can be used. I’m still uncertain about the -ngroups flag. I see at least a couple other users have asked about this but I don’t see a response. In the present case, if there are 60 slices and they are accelerated by a factor of 6, does one specify -ngroups 6 or -ngroups 10?
Joe
On Jun 2, 2019, at 19:46, Joseph Dien <jdien07@mac.commailto:jdien07@mac.com> wrote:
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Hi Doug, I’m happy to see that FreeSurfer6 provides enhanced support for slice timing. I’m trying to run it on some multi-slice data. May I ask you for some guidance on how to use the new preproc-sess options? As I understand it, I would specify “-ngroups 10” because the data were collected in ten groups of six slices at a time? I’m not sure how to specify “-sliceorder”. Slice times are below. Thanks for any help you can provide.
Joe
0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000
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Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.comhttp://joedien.com/
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Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.comhttp://joedien.com/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com