[Freesurfer] slice timing for multiband fMRI

2022-03-28 Thread Laura Doll 
External Email - Use Caution

Hi everyone,

We are currently piloting an fMRI measurement with multiband sequence on a 3T 
Siemens scanner to increase resolution, but I don't know how to do the slice 
timing correction: 
I assume, that I have to use a slicedelay file instead of the usual 
up/down/even/odd/siemens flags? But how do I know which slices were excited 
simultaneously? 

Our multiband acceleration factor is 2, if I got our MRI physicist correctly, 
GRAPPA acceleration is also 2, and we are using a TR of 2s. 
More details of the sequence are in the attached pdf (which is unfortunately in 
German).

Looking forward to any suggestions.

Best,
Laura


ep2d_bold, fmri_1-1.pdf
Description: Adobe PDF document
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Re: [Freesurfer] slice timing for multiband fMRI

2022-03-31 Thread Laura Doll 
External Email - Use Caution

Are there any suggestions regarding this topic? 


Am Montag, 28. März 2022 09:21 CEST, "Laura Doll" 
 schrieb: 
 
> External Email - Use Caution
> 
> Hi everyone,
> 
> We are currently piloting an fMRI measurement with multiband sequence on a 3T 
> Siemens scanner to increase resolution, but I don't know how to do the slice 
> timing correction: 
> I assume, that I have to use a slicedelay file instead of the usual 
> up/down/even/odd/siemens flags? But how do I know which slices were excited 
> simultaneously? 
> 
> Our multiband acceleration factor is 2, if I got our MRI physicist correctly, 
> GRAPPA acceleration is also 2, and we are using a TR of 2s. 
> More details of the sequence are in the attached pdf (which is unfortunately 
> in German).
> 
> Looking forward to any suggestions.
> 
> Best,
> Laura
 
 
 
 



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[Freesurfer] HRF with derivatives: results

2022-05-25 Thread Laura Doll 
External Email - Use Caution

Hi everyone,

I need some help regarding the SPM-HRF with two derivatives:
Where can I find the actual function that was used for the analysis? I am 
mostly interested in the peak latency, but would also appreciate if I can check 
the other parameters of the function somewhere. 

Best,
Laura


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Re: [Freesurfer] HRF with derivatives: results

2022-06-01 Thread Laura Doll 
External Email - Use Caution

Hi Doug, 

Thanks for your hint where to find the actual function.
But how can I find which values were used in my analysis? I.e. the input to 
this function?

Best,
Laura

Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve" 
 schrieb: 
 
> Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
> 
> On 5/25/2022 9:19 AM, Laura Doll wrote:
> >  External Email - Use Caution
> >
> > Hi everyone,
> >
> > I need some help regarding the SPM-HRF with two derivatives:
> > Where can I find the actual function that was used for the analysis? I am 
> > mostly interested in the peak latency, but would also appreciate if I can 
> > check the other parameters of the function somewhere.
> >
> > Best,
> > Laura
> >
> >
> > ___
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Re: [Freesurfer] HRF with derivatives: results

2022-06-03 Thread Laura Doll 
External Email - Use Caution

Okay, thanks. 
But how can I find out the influence of the derivatives used?
I also tried to check the beta.nii.gz files for three different versions of the 
analysis (-spmhrf 0 1 and 2), assuming that the weights for the derivatives 
might be saved as additional dimensions, but the dimensions were the same for 
all (163842x1x1x10).

I feel like I am missing something here, or maybe there is some mistake in my 
analysis? 
This is what I used:

mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 -notask 
-spmhrf 0 -TR 2 -polyfit 2 -analysis Test0.lh -per-run -taskreg PupAvg 1

selxavg3-sess -s S05 -analysis Test0.lh

And Test1/2 with -spmhrf 1/2, respectively.

Thanks in Advance!

Laura

 
Am Mittwoch, 01. Juni 2022 16:50 CEST, "Douglas N. Greve" 
 schrieb: 
 
> It uses the default parameters:
>    tau1 = 1;
>    tau2 = 1;
>    ttp1 = 5*tau1;  % 6 %
>    ttp2 = 15*tau1; % 16 %
>    c  = 1/6;
> 
> 
> 
> On 6/1/2022 4:27 AM, Laura Doll wrote:
> >  External Email - Use Caution
> >
> > Hi Doug,
> >
> > Thanks for your hint where to find the actual function.
> > But how can I find which values were used in my analysis? I.e. the input to 
> > this function?
> >
> > Best,
> > Laura
> >
> > Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve" 
> >  schrieb:
> >   
> >> Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
> >>
> >> On 5/25/2022 9:19 AM, Laura Doll wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Hi everyone,
> >>>
> >>> I need some help regarding the SPM-HRF with two derivatives:
> >>> Where can I find the actual function that was used for the analysis? I am 
> >>> mostly interested in the peak latency, but would also appreciate if I can 
> >>> check the other parameters of the function somewhere.
> >>>
> >>> Best,
> >>> Laura
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] HRF with derivatives: results

2022-06-07 Thread Laura Doll 
External Email - Use Caution

Yes, I think so. That would mean, that the additional frames correspond to the 
weights of the derivatives, right?

But as I mentioned in the previous mail, they do have the same dimensions (in 
matlab, checking the beta.vol).  
Do you have any idea, what could have gone wrong?
I double checked for Copy/Paste errors or stuff like that, but didn't find any.

These are the exact terminal entries from last week:

mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 -notask 
-spmhrf 1 -TR 2 -polyfit 2 -analysis TestPupAvg.lh -per-run -taskreg PupAvg 1
selxavg3-sess -s S05 -analysis TestPupAvg.lh
mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 -notask 
-spmhrf 0 -TR 2 -polyfit 2 -analysis Test0PupAvg.lh -per-run -taskreg PupAvg 1
selxavg3-sess -s S05 -analysis Test0PupAvg.lh

And I loaded the results in Matlab with
beta1 = load_nifti('./S05/bold/TestPupAvg.lh/beta.nii.gz')
beta0 = load_nifti('./S05/bold/Test0PupAvg.lh/beta.nii.gz')

Which results in equal beta1 and beta0.


Best,
Laura

Am Freitag, 03. Juni 2022 19:04 CEST, "Douglas N. Greve" 
 schrieb: 
 
> The -spmhrf 1 and 2 should have had additional frame in the beta.nii.gz. 
> Is that what you are looking at?
> 
> On 6/3/2022 4:51 AM, Laura Doll wrote:
> >  External Email - Use Caution
> >
> > Okay, thanks.
> > But how can I find out the influence of the derivatives used?
> > I also tried to check the beta.nii.gz files for three different versions of 
> > the analysis (-spmhrf 0 1 and 2), assuming that the weights for the 
> > derivatives might be saved as additional dimensions, but the dimensions 
> > were the same for all (163842x1x1x10).
> >
> > I feel like I am missing something here, or maybe there is some mistake in 
> > my analysis?
> > This is what I used:
> >
> > mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 
> > -notask -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0.lh -per-run -taskreg 
> > PupAvg 1
> >
> > selxavg3-sess -s S05 -analysis Test0.lh
> >
> > And Test1/2 with -spmhrf 1/2, respectively.
> >
> > Thanks in Advance!
> >
> > Laura
> >
> >   
> > Am Mittwoch, 01. Juni 2022 16:50 CEST, "Douglas N. Greve" 
> >  schrieb:
> >   
> >> It uses the default parameters:
> >>     tau1 = 1;
> >>     tau2 = 1;
> >>     ttp1 = 5*tau1;  % 6 %
> >>     ttp2 = 15*tau1; % 16 %
> >>     c  = 1/6;
> >>
> >>
> >>
> >> On 6/1/2022 4:27 AM, Laura Doll wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Hi Doug,
> >>>
> >>> Thanks for your hint where to find the actual function.
> >>> But how can I find which values were used in my analysis? I.e. the input 
> >>> to this function?
> >>>
> >>> Best,
> >>> Laura
> >>>
> >>> Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve" 
> >>>  schrieb:
> >>>
> >>>> Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
> >>>>
> >>>> On 5/25/2022 9:19 AM, Laura Doll wrote:
> >>>>>External Email - Use Caution
> >>>>>
> >>>>> Hi everyone,
> >>>>>
> >>>>> I need some help regarding the SPM-HRF with two derivatives:
> >>>>> Where can I find the actual function that was used for the analysis? I 
> >>>>> am mostly interested in the peak latency, but would also appreciate if 
> >>>>> I can check the other parameters of the function somewhere.
> >>>>>
> >>>>> Best,
> >>>>> Laura
> >>>>>
> >>>>>
> >>>>> ___
> >>>>> Freesurfer mailing list
> >>>>> Freesurfer@nmr.mgh.harvard.edu
> >>>>> https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt_ej_-0lwM9sGa6sE0VR22huqY8k28LeVc8UmVh9JhbA19F4S-KkN9jt-qw6MytIf9zcpxHr0Uq7jHznAs-mAgiAdqKv4ngbrpk6lr99ZeurunWbYUD4AwtyGo9qXW44fK2xyarNRcF_sVQfSfHN-abS3zKcgfeEPT0InC7ndMssP_m3gjlJjg8MKgY65KS-exNqCyu-qiCyjAZ4WFTanoXFuX47S_uHuMQwm4AqgaY5mb3fGJ0Ni09H6YoPtuieppduL6IslQTHZiKs1bn/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> >>>> ___
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://secure-web.cisco

Re: [Freesurfer] HRF with derivatives: results

2022-06-09 Thread Laura Doll 
External Email - Use Caution

Good to know, thanks!


Am Donnerstag, 09. Juni 2022 10:22 CEST, "Douglas N. Greve" 
 schrieb: 
 
> Oh,  you're using a task regressor? That will not be convolved with the 
> HRF (or its derivative). The HRF/deriv only applies to paradigm files. 
> If you want that in your task regressor, you will have to do it yourself.
> 
> On 6/7/2022 4:08 AM, Laura Doll wrote:
> >  External Email - Use Caution
> >
> > Yes, I think so. That would mean, that the additional frames correspond to 
> > the weights of the derivatives, right?
> >
> > But as I mentioned in the previous mail, they do have the same dimensions 
> > (in matlab, checking the beta.vol).
> > Do you have any idea, what could have gone wrong?
> > I double checked for Copy/Paste errors or stuff like that, but didn't find 
> > any.
> >
> > These are the exact terminal entries from last week:
> >
> > mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 
> > -notask -spmhrf 1 -TR 2 -polyfit 2 -analysis TestPupAvg.lh -per-run 
> > -taskreg PupAvg 1
> > selxavg3-sess -s S05 -analysis TestPupAvg.lh
> > mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 
> > -notask -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0PupAvg.lh -per-run 
> > -taskreg PupAvg 1
> > selxavg3-sess -s S05 -analysis Test0PupAvg.lh
> >
> > And I loaded the results in Matlab with
> > beta1 = load_nifti('./S05/bold/TestPupAvg.lh/beta.nii.gz')
> > beta0 = load_nifti('./S05/bold/Test0PupAvg.lh/beta.nii.gz')
> >
> > Which results in equal beta1 and beta0.
> >
> >
> > Best,
> > Laura
> >
> > Am Freitag, 03. Juni 2022 19:04 CEST, "Douglas N. Greve" 
> >  schrieb:
> >   
> >> The -spmhrf 1 and 2 should have had additional frame in the beta.nii.gz.
> >> Is that what you are looking at?
> >>
> >> On 6/3/2022 4:51 AM, Laura Doll wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Okay, thanks.
> >>> But how can I find out the influence of the derivatives used?
> >>> I also tried to check the beta.nii.gz files for three different versions 
> >>> of the analysis (-spmhrf 0 1 and 2), assuming that the weights for the 
> >>> derivatives might be saved as additional dimensions, but the dimensions 
> >>> were the same for all (163842x1x1x10).
> >>>
> >>> I feel like I am missing something here, or maybe there is some mistake 
> >>> in my analysis?
> >>> This is what I used:
> >>>
> >>> mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 
> >>> -notask -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0.lh -per-run -taskreg 
> >>> PupAvg 1
> >>>
> >>> selxavg3-sess -s S05 -analysis Test0.lh
> >>>
> >>> And Test1/2 with -spmhrf 1/2, respectively.
> >>>
> >>> Thanks in Advance!
> >>>
> >>> Laura
> >>>
> >>>
> >>> Am Mittwoch, 01. Juni 2022 16:50 CEST, "Douglas N. Greve" 
> >>>  schrieb:
> >>>
> >>>> It uses the default parameters:
> >>>>      tau1 = 1;
> >>>>  tau2 = 1;
> >>>>  ttp1 = 5*tau1;  % 6 %
> >>>>  ttp2 = 15*tau1; % 16 %
> >>>>  c  = 1/6;
> >>>>
> >>>>
> >>>>
> >>>> On 6/1/2022 4:27 AM, Laura Doll wrote:
> >>>>>External Email - Use Caution
> >>>>>
> >>>>> Hi Doug,
> >>>>>
> >>>>> Thanks for your hint where to find the actual function.
> >>>>> But how can I find which values were used in my analysis? I.e. the 
> >>>>> input to this function?
> >>>>>
> >>>>> Best,
> >>>>> Laura
> >>>>>
> >>>>> Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve" 
> >>>>>  schrieb:
> >>>>> 
> >>>>>> Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
> >>>>>>
> >>>>>> On 5/25/2022 9:19 AM, Laura Doll wrote:
> >>>>>>> External Email - Use Caution
> >>>>>>>
> >>>>>>> Hi everyone,
> >>>>>>>
> >>>>>>> I need some help regard