Re: [Freesurfer] multi-slice timing correction

[Greve, Douglas N.,Ph.D.]

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 
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 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
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000



Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://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.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.com


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Re: [Freesurfer] multi-slice timing correction

[Joseph Dien]

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  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 > > 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
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 
>> 
>> 
>> 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
> 
> 
> 
> 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



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
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Re: [Freesurfer] multi-slice timing correction

[Joseph Dien]

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  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
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 
> 
> 
> 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



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

[Freesurfer] multi-slice timing correction

[Joseph Dien]

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
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000



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
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