External Email - Use Caution
Hi,
Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed, I'll describe them again:
I want to run an analysis with the normalized pupil size as task regressor. Because the pupil dilation response itself is already slow (peaking after ~1s), we thought it would be good to use FIR instead of assuming a certain shape of HRF.
I tried two different analysis:
1) mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run -taskreg PupPAvg 1
2) same with "-event-related -nc 2 -paradigm paradigm.txt" instead of -notask.
With 1), the analysis does run without errors but I don't get to see a time course when plotting with tksurfer-sess and I don't know what exactly is plotted than (the maximum or the first time point or...?).
With 2) I arrive at a similar point as in February: when I try to plot the results, I get this error:
ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h
The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and rename the copy to h.nii.gz, tksurfer-sess opens including the time course viewer. But this shows does not show a time course.
So the question is: How do I get time courses for this FIR analysis with a task regressor? Where is my mistake?
And a slightly off-topic question regarding task regressors & slice timing:
As far as I know, stc shifts all slices to TR/2 and with the default stimulus delay parameter, TR/2 is also added to the times in paradigm files. But how does it work for task regressors? Do I have to give "corrected" values? I.e. in my case I average the pupil size over TR in order to arrive at the desired number of time points. But should I do that around the original start of the sequence or around the "corrected" time (i.e. +TR/2)?
Many thanks in advance,
Laura
On 2/5/2021 2:08 AM, Doll, Laura wrote:
External Email - Use Caution
Hi Doug,
Thanks for your response. No, I did not demean the task regressor... do I have to?
Yea, probably a good idea
Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point. Not sure here (have not run FIR in a long time). I noticed that you have -notask on your mkanalysis command. Have you tried it without -notask? I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows. Depends on the contrast, but I think it should create maps for each time point in the FIR window.
Best, Laura
Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems?
On 2/3/2021 8:32 AM, Doll, Laura wrote:
External Email - Use Caution
Hi everyone,
Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related).
This works when I use "-spmhrf" or other HRF options.
However, for FIR I cannot get the expected time course in the single subjects data.
Tksurfer ends with an error because it cannot find the file h.nii.gz:
ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h
This file indeed does not exist, there is only one called "h-offset".
The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1
selxavg3-sess -s S01_3 -analysis PupilFIR.lh
tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer
Is there any solution for this? Or any reason why it should not be done that way?
Best, Laura
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The FIR analysis can only be used with a task. It sounds like you want to deconvolve the HRF with the pupil diameter? This can be done, but it is tricky (can't just use FIR). You'd have to create a special task regressor where you have multiple columns. The first column would be the current task regressor. The next column would be the current regressor shifted down one (put a 0 in the first slot). Keep adding regressors to cover about 20-26 seconds (each regressor covers one TR). Then the beta values for these regressors will be the FIR you want. To visualize, you'd have to set up an F contrast (mkcontrast-sess), and then load the ces.nii.gz file
On 7/12/2021 6:55 AM, Doll, Laura wrote:
External Email - Use Caution
Hi,
Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed, I'll describe them again:
I want to run an analysis with the normalized pupil size as task regressor. Because the pupil dilation response itself is already slow (peaking after ~1s), we thought it would be good to use FIR instead of assuming a certain shape of HRF.
I tried two different analysis:
- mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm
5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run -taskreg PupPAvg 1
- same with "-event-related -nc 2 -paradigm paradigm.txt" instead of
-notask.
With 1), the analysis does run without errors but I don't get to see a time course when plotting with tksurfer-sess and I don't know what exactly is plotted than (the maximum or the first time point or...?).
With 2) I arrive at a similar point as in February: when I try to plot the results, I get this error:
ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h
The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and rename the copy to h.nii.gz, tksurfer-sess opens including the time course viewer. But this shows does not show a time course.
So the question is: How do I get time courses for this FIR analysis with a task regressor? Where is my mistake?
And a slightly off-topic question regarding task regressors & slice timing:
As far as I know, stc shifts all slices to TR/2 and with the default stimulus delay parameter, TR/2 is also added to the times in paradigm files. But how does it work for task regressors? Do I have to give "corrected" values? I.e. in my case I average the pupil size over TR in order to arrive at the desired number of time points. But should I do that around the original start of the sequence or around the "corrected" time (i.e. +TR/2)?
Many thanks in advance,
Laura
On 2/5/2021 2:08 AM, Doll, Laura wrote:
External Email - Use Caution Hi Doug, Thanks for your response. No, I did not demean the task regressor... do I have to?Yea, probably a good idea
Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point.Not sure here (have not run FIR in a long time). I noticed that you have -notask on your mkanalysis command. Have you tried it without -notask?
I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows.Depends on the contrast, but I think it should create maps for each time point in the FIR window.
Best, Laura Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems? On 2/3/2021 8:32 AM, Doll, Laura wrote: External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related). This works when I use "-spmhrf" or other HRF options. However, for FIR I cannot get the expected time course in the single subjects data. Tksurfer ends with an error because it cannot find the file h.nii.gz: ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist, there is only one called "h-offset". The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 selxavg3-sess -s S01_3 -analysis PupilFIR.lh tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer Is there any solution for this? Or any reason why it should not be done that way? Best, Laura _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1n9wxgcJ7Tc0qfJejA8xVei3ZUL3PGBbuAJFZvOdieNEW7iV3ZbMzdVhv4lC-uc4nEYLide19Pc8nUP8g2YdCpazfG6inF7-GziFwkMe4aoCVV4Q5B-6a1Tx514-oH4sz1XTqb9SeQtRqw5iOOJqhEgVLtw7vm8oQaiwmAYak8IzUz35o-7YSWAe-prjMZe55-frNPqu4wf20d1eVJhg_0lbOpF7rnK7gRbr5IYXFU4n2f2IAb7ErVU0tD8XEqCr3MnS8TuKgvE_-DruiZJ66gg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1n9wxgcJ7Tc0qfJejA8xVei3ZUL3PGBbuAJFZvOdieNEW7iV3ZbMzdVhv4lC-uc4nEYLide19Pc8nUP8g2YdCpazfG6inF7-GziFwkMe4aoCVV4Q5B-6a1Tx514-oH4sz1XTqb9SeQtRqw5iOOJqhEgVLtw7vm8oQaiwmAYak8IzUz35o-7YSWAe-prjMZe55-frNPqu4wf20d1eVJhg_0lbOpF7rnK7gRbr5IYXFU4n2f2IAb7ErVU0tD8XEqCr3MnS8TuKgvE_-DruiZJ66gg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Yes, that's exactly what I want. Thanks for the explanation!
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU Gesendet: Donnerstag, 15. Juli 2021 18:05 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction
The FIR analysis can only be used with a task. It sounds like you want to deconvolve the HRF with the pupil diameter? This can be done, but it is tricky (can't just use FIR). You'd have to create a special task regressor where you have multiple columns. The first column would be the current task regressor. The next column would be the current regressor shifted down one (put a 0 in the first slot). Keep adding regressors to cover about 20-26 seconds (each regressor covers one TR). Then the beta values for these regressors will be the FIR you want. To visualize, you'd have to set up an F contrast (mkcontrast-sess), and then load the ces.nii.gz file
On 7/12/2021 6:55 AM, Doll, Laura wrote:
External Email - Use Caution
Hi,
Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed, I'll describe them again:
I want to run an analysis with the normalized pupil size as task regressor. Because the pupil dilation response itself is already slow (peaking after ~1s), we thought it would be good to use FIR instead of assuming a certain shape of HRF.
I tried two different analysis:
1) mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run -taskreg PupPAvg 1
2) same with "-event-related -nc 2 -paradigm paradigm.txt" instead of -notask.
With 1), the analysis does run without errors but I don't get to see a time course when plotting with tksurfer-sess and I don't know what exactly is plotted than (the maximum or the first time point or...?).
With 2) I arrive at a similar point as in February: when I try to plot the results, I get this error:
ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h
The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and rename the copy to h.nii.gz, tksurfer-sess opens including the time course viewer. But this shows does not show a time course.
So the question is: How do I get time courses for this FIR analysis with a task regressor? Where is my mistake?
And a slightly off-topic question regarding task regressors & slice timing:
As far as I know, stc shifts all slices to TR/2 and with the default stimulus delay parameter, TR/2 is also added to the times in paradigm files. But how does it work for task regressors? Do I have to give "corrected" values? I.e. in my case I average the pupil size over TR in order to arrive at the desired number of time points. But should I do that around the original start of the sequence or around the "corrected" time (i.e. +TR/2)?
Many thanks in advance,
Laura
On 2/5/2021 2:08 AM, Doll, Laura wrote:
External Email - Use Caution
Hi Doug,
Thanks for your response. No, I did not demean the task regressor... do I have to?
Yea, probably a good idea
Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point. Not sure here (have not run FIR in a long time). I noticed that you have -notask on your mkanalysis command. Have you tried it without -notask? I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows. Depends on the contrast, but I think it should create maps for each time point in the FIR window.
Best, Laura
Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems?
On 2/3/2021 8:32 AM, Doll, Laura wrote:
External Email - Use Caution
Hi everyone,
Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related).
This works when I use "-spmhrf" or other HRF options.
However, for FIR I cannot get the expected time course in the single subjects data.
Tksurfer ends with an error because it cannot find the file h.nii.gz:
ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h
This file indeed does not exist, there is only one called "h-offset".
The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1
selxavg3-sess -s S01_3 -analysis PupilFIR.lh
tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer
Is there any solution for this? Or any reason why it should not be done that way?
Best, Laura
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Hi Doug,
I run into some questions while trying to do this analysis: How do you set up the contrast you suggested? Since there is no paradigm file, I don't know what I should enter as conditions.
But on the other hand, I automatically get ces.nii.gz for the task regressor in the single subjects. Those do have 12 columns/time points that I can visualize with tksurfer. After isxconcat-sess of the group, I have 12 different ces/cesvar files in the output folder: from ces.000.nii.gz up to ces.011.nii.gz. Are those already the files that I need? Or would I get something else with the contrast that you mentioned?
Best, Laura
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Doll, Laura Laura.Doll@med.uni-heidelberg.de Gesendet: Freitag, 16. Juli 2021 08:08 An: Freesurfer support list Betreff: Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction
External Email - Use Caution
Yes, that's exactly what I want. Thanks for the explanation!
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU Gesendet: Donnerstag, 15. Juli 2021 18:05 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction
The FIR analysis can only be used with a task. It sounds like you want to deconvolve the HRF with the pupil diameter? This can be done, but it is tricky (can't just use FIR). You'd have to create a special task regressor where you have multiple columns. The first column would be the current task regressor. The next column would be the current regressor shifted down one (put a 0 in the first slot). Keep adding regressors to cover about 20-26 seconds (each regressor covers one TR). Then the beta values for these regressors will be the FIR you want. To visualize, you'd have to set up an F contrast (mkcontrast-sess), and then load the ces.nii.gz file
On 7/12/2021 6:55 AM, Doll, Laura wrote:
External Email - Use Caution
Hi,
Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed, I'll describe them again:
I want to run an analysis with the normalized pupil size as task regressor. Because the pupil dilation response itself is already slow (peaking after ~1s), we thought it would be good to use FIR instead of assuming a certain shape of HRF.
I tried two different analysis:
1) mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run -taskreg PupPAvg 1
2) same with "-event-related -nc 2 -paradigm paradigm.txt" instead of -notask.
With 1), the analysis does run without errors but I don't get to see a time course when plotting with tksurfer-sess and I don't know what exactly is plotted than (the maximum or the first time point or...?).
With 2) I arrive at a similar point as in February: when I try to plot the results, I get this error:
ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h
The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and rename the copy to h.nii.gz, tksurfer-sess opens including the time course viewer. But this shows does not show a time course.
So the question is: How do I get time courses for this FIR analysis with a task regressor? Where is my mistake?
And a slightly off-topic question regarding task regressors & slice timing:
As far as I know, stc shifts all slices to TR/2 and with the default stimulus delay parameter, TR/2 is also added to the times in paradigm files. But how does it work for task regressors? Do I have to give "corrected" values? I.e. in my case I average the pupil size over TR in order to arrive at the desired number of time points. But should I do that around the original start of the sequence or around the "corrected" time (i.e. +TR/2)?
Many thanks in advance,
Laura
On 2/5/2021 2:08 AM, Doll, Laura wrote:
External Email - Use Caution
Hi Doug,
Thanks for your response. No, I did not demean the task regressor... do I have to?
Yea, probably a good idea
Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point. Not sure here (have not run FIR in a long time). I noticed that you have -notask on your mkanalysis command. Have you tried it without -notask? I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows. Depends on the contrast, but I think it should create maps for each time point in the FIR window.
Best, Laura
Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems?
On 2/3/2021 8:32 AM, Doll, Laura wrote:
External Email - Use Caution
Hi everyone,
Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related).
This works when I use "-spmhrf" or other HRF options.
However, for FIR I cannot get the expected time course in the single subjects data.
Tksurfer ends with an error because it cannot find the file h.nii.gz:
ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h
This file indeed does not exist, there is only one called "h-offset".
The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1
selxavg3-sess -s S01_3 -analysis PupilFIR.lh
tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer
Is there any solution for this? Or any reason why it should not be done that way?
Best, Laura
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Doll, Laura -
Douglas N. Greve