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"
<dgr...@mgh.harvard.edu> 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"
> > <dgr...@mgh.harvard.edu> 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"
> >>> <dgr...@mgh.harvard.edu> 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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