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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:
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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:
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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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