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:
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<mailto: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
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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<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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
