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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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Hi Rick,
I've got the average global connectivity of all voxels for each subject now based on your help. Now how can I get the corrleation between each voxel and all other brain voxel in order to be able to do one sample ttest on all the brain voxels. I guess I should use this command : 3dTcorrMap ? is that correct? if yes how I should run this command?
Thanks,
Aral
by
aral.ahmadi
-
AFNI Message Board
I've got the average global connectivity of all voxels for each subject now based on your help. Now how can I get the corrleation between each voxel and all other brain voxel in order to be able to do one sample ttest on all the brain voxels. I guess I should use this command : 3dTcorrMap ? is that correct? if yes how I should run this command?
Thanks,
Aral
by
aral.ahmadi
-
AFNI Message Board
Hi Rick,
Just one more question. I've got the average global connectivity of all voxels for each subject now based on your help. Now how can I get the corrleation between each voxel and all other brain voxel in order to be able to do one sample ttest on all the brain voxels. I guess I should use this command : 3dTcorrMap ? is that correct? if yes how I should run this command?
Thanks,
by
aral.ahmadi
-
AFNI Message Board
Hi Rick,
So now what i have is a single volume, where each voxel
has the average correlation of that voxel with
every other voxel in the brain. so now how can i get a a single value for each subject,
which would be the average of the above values
across the brain?
Thanks,
Aral
by
aral.ahmadi
-
AFNI Message Board
Ok i've got my output as a nifti file now. It might sound stupid but how from this output file I can read the global connectivity for each subject or each voxel? I mean I expected see the numbers for each voxels or each subjects but all i can see is a a nonreadable signs.
Rick thanks so much for your help.
by
aral.ahmadi
-
AFNI Message Board
Hi Rick, thanks yes I noticed that right after i sent you the message . I have a problem though about the type of output file, they are BRIK file (mean.brain.corr+tlrc.BRIK) and (mean.brain.corr+tlrc.HEAD) ! is that because I used the nifti file not tlrc file as input ? and also my mask file was in hdr. so I am not sure if I can use hdr and nifti file in these commands as input. you could see ho
by
aral.ahmadi
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AFNI Message Board
Hi Rick,
I ran all these commands on one of my subject to see how it works (each of my subject has 50 slices)
(3dTnorm -prefix unit.data DATA+tlrc
3dmaskave -quiet -mask BRAIN_MASK+tlrc DATA+tlrc > brain.mean.1D
3dTcorr1D -prefix mean.brain.corr DATA+tlrc brain.mean.1D)
the result i get is 50 numbers for each subject, so it seems it calculate the global connectivity for each slice not vox
by
aral.ahmadi
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AFNI Message Board
Hi Rick, thanks for answering. I want a single volume, where each voxel
has the average correlation of that voxel with every other voxel in the brain for each subject.
Thanks,
Aral
by
aral.ahmadi
-
AFNI Message Board
Hi,
I am trying to calculate global connectivity for each subject by instacorr but dont know how. Is anybody out there can help me. Thanks,
Aral
by
aral.ahmadi
-
AFNI Message Board