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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
History of AFNI updates
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Pages: 12
Results 31 - 41 of 41
Hi,
I have questions about scaling in the first level analysis by running afni_proc.py.
1) Does 'scaling' mean percent signal change calculation?
2) fMRI raw data value can have negative value? or all value 0 or positive value? When I see 'proc.$subject.glt' file, the 'scale' part is saying that
# ================================= scale ===================
by
chaj
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AFNI Message Board
Thanks, Paul
3dClusterize command worked well to get the clusterized image. But using @chauffeur_afni still give me some errors for example, only showing very white anatomical image even though I already changed the range setup of it or some conflict with using tcsh.
Now I just combine 3dClusterize and 'Afni -com', and it worked well to save images.
Thanks again.
-Jung
by
chaj
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AFNI Message Board
Hi,
I am trying to save images from the 3dLME results with 3dClustsim clusterized.
My Afni command is
afni -com 'SET_XHAIRS A.OFF' \
-com 'OPEN_WINDOW A.axialimage mont=3x5:4' \
-com 'OPEN_WINDOW A.sagittalimage mont=3x5:4' \
-com 'SWITCH_UNDERLAY A.avg152T1_2p5.nii' \
-com 'SWITCH_OVERLAY A.output.myLME+tlrc' \
-com 'SET_F
by
chaj
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AFNI Message Board
The standard is really to use a voxelwise p=0.001 threshold (though p=0.002 does look reasonable, too)
-> p=0.002 looks reasonable. Everyone knows p=0.001 is fine. But p=0.002 looks unusual, so is there any reference or proof for using p=0.002?
by
chaj
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AFNI Message Board
Thanks Gang.
If I make the gender as categorical variable, it is going to be a factor. right?
We usually have been regressing out the gender variable as covariates.
The contrast means the contrast between two conditions. In my case for GoNogo task, the contrast is the same as Condition : 1*Nogo -1*Go'
Jung
by
chaj
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AFNI Message Board
I am trying to run 3dMVM with
Between-subject factor : group (G1, G2, G3, and G4), scanner (scan1 and scan2),
Quantitative Covariates : gender, age, and accuracy
I am using the contrast obtained from SPM instead of the beta images. I am trying to get the average effect similar to what we get from SPM.
In SPM when we look at the average effect F stat-map, it seems like the covariates are
by
chaj
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AFNI Message Board
We estimate the cluster wise threshold using 3dClustsim with ACF options, and look at the results at voxelwise p=0.01, the cluster size threshold is estimated by 3dClustsim with ACF options. In that case, is it okay that we still look at p=0.01?
by
chaj
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AFNI Message Board
Hi, all
I have question about deciding voxelwise p-value by using 3dClustsim -acf.
According to AFNI handout(Clusterizing), we need to use voxelwise p-value which is less than 0.002 with mixed ACF.
Is it acceptable to use voxelwise p=0.01 or other bigger value? About this issue, if you have a reference, could you let me know?
Thanks
Jung
by
chaj
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AFNI Message Board
Hi,
I have questions when I run afni_proc.py example 11b since I am trying to use MNI space instead of Talairach space
This is my afni_proc.py
afni_proc.py -subj_id FT.11b.rest \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat My_anat+orig \
by
chaj
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AFNI Message Board
Hi,
I am trying to make a resting state analysis pipeline. I tried to run afni_proc.py example 11.
Freesurfer is used for parcellation from an anatomical image. I am going to fit this parcellation on the epi functional images as well. In my knowledge, the functional image parcellation is different with the anatomical image parcellation, so that’s why my lab have been using the Craddock templ
by
chaj
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AFNI Message Board
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Pages: 12