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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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How do I know which clusters are positive and which ones are negative when using 'bi-sided' option in Clusterize in AFNI GUI? I am only able to see the number of positive and negative clusters. If the number of the resulting clusters is 5, it only reports 2 positive and 3 negative but not which ones. I would also like to save +ve/-ve when saving the table from the report.
Any help is
by
umeshksingla
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AFNI Message Board
This reply helps a lot. My query is (which might be silly), since you said:
"""
- Such a cluster table is produced by 3dttest++ -Clustsim,
though it is up to you to apply the threshold/cluster step
(it does not assume which p-values to apply).
- The thresholding and clustering is applied to a t-stat or
z-score volume. The mean volume would probably be used for
color
by
umeshksingla
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AFNI Message Board
Well, I only have the subjects' data in MNI space which I believe couldn't be converted back to the original natives' space without other information (anat data etc., but I am not very sure at this point). So I created spherical regions using:
echo “23.23 -4.37 -18.13” | 3dUndump -prefix sub1_masks/subX_rAmygdala -master subX+tlrc. -srad 3 -xyz -
where X=1..40.
You menti
by
umeshksingla
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AFNI Message Board
While creating correlation maps using 3dTcorr1D, are you sure you should be using -mask option for a standard seed correlation analysis procedure? unless it is intended to mask some another region..
by
umeshksingla
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AFNI Message Board
To add (to the confusion), changing view using 3drefit doesn't work on .nii files unless you change the space while it works when you first 3dcopy .nii files to HEAD/BRIK and then do `3drefit -view`. Idk why.
by
umeshksingla
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AFNI Message Board
I'm trying to do seed correlation analysis. I have .nii files of 20 subjects each of controls and patients. While creating a spherical mask do I need to create a mask for each subject? or can I create a mask from any template and then use the same for all subjects? If just one mask can work on all subjects, then what is the best master dataset for that? i.e., suppose I want to extract time s
by
umeshksingla
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AFNI Message Board