External Email - Use Caution
Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts between runs
Background
Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).
I performed the preprocessing and 1st levels stats in the native subjects space
Questions
* How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session? * Can I obtain this within-subject contrast by staying in the native subject space? * Do I have to concatenate both runs and create a new parradigm file?
Thanks for your support
Sincerely
Chris
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts between runs
*Background*
Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).
I performed the preprocessing and 1st levels stats in the native subjects space
*Questions*
- How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session?
The easiest way is to code the conditions differently in the paradigm file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just create contrasts as normal
- Can I obtain this within-subject contrast by staying in the native subject space?
It can be done in fsaverage or the native subject surface space, it is not related.
- Do I have to concatenate both runs and create a new parradigm file?
No, see above
Thanks for your support
Sincerely
Chris
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Mr. Greve
Thanks for your suggestions.
However I'm still a bit puzzled about how to contrast two runs corresponding to different stimulations (StimA: runA and StimB:runB) from one subject.
I have two runs each containing a paradigm file corresponding to one of the two stimulations.
How is it possible to contrast those two stimulation conditions acquired in two different runs since one run and thus also the paradigm file does not contain both stimulation conditions?
Seemingly both stimulation conditions must be in one paradigm file set to different onset timings to perform mkcontrast-sess
My folder Structure is as follows
Project Name
Session = Subject
Runs (001, 002) = Stimulation A and Stimulation B, each with a separate paradigm file
I know that I do not have to model the no-stimulation periods explicitely
Best wishes
Chris
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@mgh.harvard.edu Gesendet: Freitag, 6. März 2020 17:54:16 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] within-subject contrast between runs
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts between runs
Background
Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).
I performed the preprocessing and 1st levels stats in the native subjects space
Questions
* How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session?
The easiest way is to code the conditions differently in the paradigm file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just create contrasts as normal
* Can I obtain this within-subject contrast by staying in the native subject space?
It can be done in fsaverage or the native subject surface space, it is not related.
* Do I have to concatenate both runs and create a new parradigm file?
No, see above
Thanks for your support
Sincerely
Chris
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In par file for the A run, you say that the condition number is 1; in the par file for run B, say that the condition is number 2 (so condition 2 does not appear in run 1's parfile, and condition 1 does not appear in run 2's). The in mkcontrast-sess, just select -a 1 -c 2
On 3/11/2020 1:42 PM, Milde, Christopher wrote:
External Email - Use Caution
Dear Mr. Greve
Thanks for your suggestions.
However I'm still a bit puzzled about how to contrast two runs corresponding to different stimulations (StimA: runA and StimB:runB) from one subject.
I have two runs each containing a paradigm file corresponding to one of the two stimulations.
How is it possible to contrast those two stimulation conditions acquired in two different runs since one run and thus also the paradigm file does not contain both stimulation conditions?
Seemingly both stimulation conditions must be in one paradigm file set to different onset timings to perform mkcontrast-sess
My folder Structure is as follows
Project Name
Session = Subject
Runs (001, 002) = Stimulation A and Stimulation B, each with a separate paradigm file
I know that I do not have to model the no-stimulation periods explicitely
Best wishes
Chris
*Von:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@mgh.harvard.edu *Gesendet:* Freitag, 6. März 2020 17:54:16 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] within-subject contrast between runs
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts between runs
*Background*
Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).
I performed the preprocessing and 1st levels stats in the native subjects space
*Questions*
- How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session?
The easiest way is to code the conditions differently in the paradigm file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just create contrasts as normal
- Can I obtain this within-subject contrast by staying in the native subject space?
It can be done in fsaverage or the native subject surface space, it is not related.
- Do I have to concatenate both runs and create a new parradigm file?
No, see above
Thanks for your support
Sincerely
Chris
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Milde, Christopher