External Email - Use Caution 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 <jdie...@mac.com> wrote: > > External Email - Use Caution > > > 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 <jdie...@mac.com >> <mailto:jdie...@mac.com>> wrote: >> >> External Email - Use Caution >> >> >> 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 >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, PhD >> Senior Research Scientist >> Department of Human Development and Quantitative Methodology >> University of Maryland, College Park >> http://joedien.com <http://joedien.com/> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------------------------------------------------------------------------- > > Joseph Dien, PhD > Senior Research Scientist > Department of Human Development and Quantitative Methodology > University of Maryland, College Park > http://joedien.com <http://joedien.com/> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
