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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
Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
On 5/25/2022 9:19 AM, Laura Doll wrote:
External Email - Use CautionHi 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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" dgreve@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 CautionHi 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...
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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 CautionHi 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" dgreve@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 CautionHi 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...
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DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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" dgreve@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 CautionHi 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" dgreve@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 CautionHi 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...
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DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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 CautionOkay, 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" dgreve@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 CautionHi 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" dgreve@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 CautionHi 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...
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DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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" dgreve@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 CautionOkay, 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" dgreve@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 CautionHi 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" dgreve@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 CautionHi 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...
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DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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 CautionYes, 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" dgreve@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 CautionOkay, 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" dgreve@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 CautionHi 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" dgreve@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p... <https://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p...
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External Email - Use Caution
Good to know, thanks!
Am Donnerstag, 09. Juni 2022 10:22 CEST, "Douglas N. Greve" dgreve@MGH.HARVARD.EDU 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 CautionYes, 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" dgreve@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 CautionOkay, 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" dgreve@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 CautionHi 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" dgreve@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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt... > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1xTlG-Uyb1U2QOCkOd7SM_GM-P5ioVq3Xn-ZIBk2jMCvLgt... > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p... <https://secure-web.cisco.com/1rmpvCcfVFDGqLo0LGNPuBTY2MFdv4E2_gcyoqa-EMXdV9p... DoGDj14oKEg1F/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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