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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
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Thank you Ziad and Rick!
I think I understand why the standard deviation from independent t test was different from 3dttest++ now.
When we run the two sample t test, the beta value in that ROI is a single number with a standard deviation of zero.
When we run 3dttest++, it is voxel-wise test, the beta value in that ROI is a mean of lots of voxels with a standard deviation not equals zero.
by
Kai
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AFNI Message Board
The above Mean (mean of Group A = 0.095, mean of Group B = 0.045) was from the afni plot.
Actually when I checked these mean values using 3dMean or taking the sub brick of the 3dttest, the mean values are identical as those from the independent two sample t test ( mean of Group A = 0.117, mean of Group B = 0.057, df =30 ).
The difference is t score. t from independent two sample t test in
by
Kai
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AFNI Message Board
Hello,
I have a question about 3dROIstats.
I used 3dROIstats to get beta values within a ROI (162 voxels) for two groups, then I run an independent two sample t test and got a t-vaule of 2.0881 ( mean of Group A = 0.117, mean of Group B = 0.057, df =30 )
However, when I run a 3dttest++ for these two groups, I got a different t-values of 1.839 within this ROI (mean of Group A = 0.095, me
by
Kai
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AFNI Message Board
Thanks Ziad,
Can I use 3dUnifize for surface creation?
Thank you very much.
Kai
by
Kai
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AFNI Message Board
Hello,
Does anyone know how to use 3dQwarp for surface creation? and how to add 3dQwarp to afni_restproc.py?
Thanks.
Kai
by
Kai
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AFNI Message Board
Thank you very much Nick, I tried using this :
3dcalc \
-a anat_1+orig \
-expr 'a*step(x-5.628)*step(15.003-x)*step(y-47.008)*step(53.57-y)*step(z+3.9)*step(-3.8-z)' \
-prefix mask_test
I didn't see the error message, but when I check the overlay mask in afni, there is nothing, do you know what is the problem?
Thank you again for you help.
Kai
by
Kai
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AFNI Message Board
Hello Daniel,
Thank you for your response.
Can you check if the following commands are right?
3dcalc \
-a anat_1+orig \
-expr 'a*step(x-5.628)*step(15.003-x)*step(y-47.008)*step(53.57-y)*equals(z,-3.878)' \
-prefix mask_test
There is no mask there, I got the following error:
*+ WARNING: output sub-brick 0 is all zeros!
And can you show me how to use 3dZeropad to cr
by
Kai
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AFNI Message Board
Hello,
I am trying to create a square mask in a single subject's original anatomical brain image, the square I need is:
x = 5.628 -- 15.003
y = 53.570 -- 47.008
z = -3.878
Can anyone show me how to create this mask using 3dcalc command?
Thanks.
Kai
by
Kai
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AFNI Message Board
Such a quick and helpful response!
Thank you very much Gang!
Kai
by
Kai
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AFNI Message Board
Hello,
# I tried to use 3dMEMA to compare group effect of a contrast. there are 18 subjects in each group.
# This is the 3dMEMA commands I used:
3dMEMA -prefix 3dMEMA.G1_VS_G2 \
-jobs 6 \
-mask mask+tlrc \
-groups G1 G2 \
-set contrast_G1 \
S1 G1_S1_REML+tlrc'[#0_Coef]' G1_S1_REML+tlrc'[#0_Tstat]' \
...
S18 G1_S18_REML+tlrc'[#0_Coef]' G1_S18_REML+tl
by
Kai
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AFNI Message Board