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Dear AFNI users-
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Hello all,
I have a subject which we scanned twice and I would like to compare the experimental task (A) vs the control task (B) on day1 vs day2. So something like . I'm not sure how to code that in 3dDeconvolve using the gltsym. I tried: A1 -B1 -A2 +B2 which seems odd.
But arithmetically it works, but I'd like to ensure the stats are also computed accordingly.
thanks
by
pbedard
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AFNI Message Board
Hi Rick,
OK I now think I understand what to do and how. >:D<
Thanks a lot for your time
pat
by
pbedard
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AFNI Message Board
Rick,
We have a Siemens scanner and these are the DICOM
We had TR=1.5 sec, 63 slices and MB=3.
This is what dicom_hdr -slice_times" returns:
-- Siemens timing (63 entries): 0.0 775.0 70.0 845.0 142.5 917.5 212.5 987.5 282.5 1057.5 352.5 1127.5 422.5 1197.5 492.5 1270.0 565.0 1340.0 635.0 1410.0 705.0 0.0 775.0 70.0 845.0 142.5 917.5 212.5 987.5 282.5 1057.5 352.5 1127.5 422.5 1197.5 4
by
pbedard
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AFNI Message Board
Hi Rick,
I found out about the offsets.
You seem to recommend I compute those times myself instead of taking them from the DICOM files?
How do I put that info back into the dataset ?
pat
by
pbedard
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AFNI Message Board
Hello Rick,
1) You seem to suggest I compute "manually" the timing offset instead of obtaining it via the dicom_hdr -slice_times of a DICOM file?
2) I'm not sure what to do after computing those times Should I put it back in the header with the @slice_times.txt in to3d and then use 3dTshift with the -tpattern @slice_times.txt option to actually time shift the timeseries?
by
pbedard
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AFNI Message Board
Hello all,
After running the program dcm2niix_afni with this command : dcm2niix_afni *, I realized that the offset in slice acquisition time are set to 0 (3dinfo -slice_timing dset+tlrc). Is this really the case that the timing offset has been corrected? I don't see any info about that in the dcm2niix_afni documentation. Then, when I run 3dvolreg with the -tshift flag the program sa
by
pbedard
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AFNI Message Board
Hi
Have you tried with +tlrc datset.
It once fixed a problem I had using a nii.gz file.
by
pbedard
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AFNI Message Board
Hi Gang,
I see in various websites and publications that people used different formula, e.g.,
2*t_stat / sqrt(n-2)
Also, my t-test is a paired one, should I account for that? I saw somewhere (Dunlop, Cortina, Vaslow & Burke (1996, S. 171) ) that I could adjust the effect size using the correlation between the two samples: t.stat * sqrt((2*(1-R)/(n-1))); R is correlation
thanks
by
pbedard
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AFNI Message Board
Hello all,
I ran t-test using 3dMEMA and would like to report the effect size as Cohen (1988).
I can't really use the beta weights since 3dMEMA weights them according to their t-stats.
How do I go about computing these effect size?
thanks
pat
by
pbedard
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AFNI Message Board
Rick and Gang,
Thanks but I'm getting more confused!!!
What do you mean by baseline?
Also, I have 4 conditions and rest in between, so my model has 5 predictors (plus the motion parameters). So these 5 predictor are in the -stim_times while motion params are in -stim_file.
Should I model it like that??
thanks
pat
by
pbedard
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AFNI Message Board
Hi Gang
So I would put the rest period as a -stim_file?
Should have 1 file with all the times of the rest or many files ?? You seem to indicate that there should be many???
thanks,
pat
by
pbedard
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AFNI Message Board
Hi Rick,
I'd like to have the statistic of the contrast at the subject level, since I will not have enough subject for group analysis.
How do I code that in 3dDeconvolve -gltsym ?
pat
by
pbedard
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AFNI Message Board
Rick,
Simple contrast after the decon?
I'd like to have a contrast at the subject level so I' think it needs to be done within the decon...
-pat
by
pbedard
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AFNI Message Board
Hi Rick
It's baseline...it is of interrest as it seems Rest has changed from D1 to D2, therefore I think I need to contrast A with Rest before comparing across both A-D1 and A-D2.
by
pbedard
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AFNI Message Board
Hello afni'ers,
In our experiment we have scanning sessions on 2 different days that are similar and I want to contrast conditions A-Day1 vs conditions A-Day2. So first I though of concatenating both timseries and contrast between A-Day1 vs A-Day2 conditions directly. However, I first have to contrast the A condition with rest on each day (A-Day1 vs Rest and A-Day2 vs Rest) before doing
by
pbedard
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AFNI Message Board
Hello,
I am using 3dttest++ for a between group ttest with 14 subjects in each group.
But depending on how I write the script the degrees of freedom change which makes me think the t-test used was a paired or unpaired.
3dttest++ -prefix ../anova/ttest_AAA-BBB \
-setA AAA \
s1_A+tlrc \
..
s15_A+tlrc \
\
-setB BBB \
s1_B+tlrc \
..
s15_B+tlrc \
This results in df = 12, which is i
by
pbedard
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AFNI Message Board