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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 so much!
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> Hi-
>
> Assuming you have mapped your Freesurfer-created
> ROIs into the space of the FMRI data, then I think
> 3dNetCorr will do what you want. You can
> calculate the correlation matrix (default), as
> well as output the average time series ("-ts_out")
> of each region. If
by
jtang
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AFNI Message Board
Hello,
I have both T1 data and resting fmri data. The resting fmri data is processed with afni_proc.py My T1 data is processed with Freesurfer. I have created an atlas for each subject with 68 cortical regions and 8 subcortical regions. How can I use this subject specific atlas to calculate the ROI-to-ROI correlation and then create an 82*82 matrix? and the mean timecourse of each ROIs?
by
jtang
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AFNI Message Board
Hi Gang,
Thank you so much!
I tried both r and z :
3dTcorrMap -input input_data -mask mask_data -Cexpr 'step(r)*r' r_output_data
3dTcorrMap -input input_data -mask mask_data -Cexpr 'step(z)*z' z_output_data
But, the values in the z_output_data seems a slightly higher than that in the r_output_data. So, what is the difference between these two?
Thanks,
Jins
by
jtang
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AFNI Message Board
Hello,
I want to use 3dTcorrMap to calcualte the global connectivity.
Given that mixed positive and negative value could cancel each other( eg average 0.1 and -0..1). so I want to average positive correaltion and negative correlation separately.
3dTcorrMap -input input_data -mask mask_data -Cexpr 'step(z-0)*z' output_data ( for Zmean)
3dTcorrMap -input input_data -ma
by
jtang
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AFNI Message Board
Hello,
Is it possible to use 3ddegreecentrality to calculate the global connectivity (the unthreholded weighted degree centrality ) ? I want to average the positive and negative correlation separately.
Thanks,
Jinsong
by
jtang
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AFNI Message Board
Hello ,
I was wondering if there was a way to split multi-brick bucket file into single sub-brick file? I have some output files from 3ddegreecentrality. Each of them has 2 sub-bricks. I have try fslsplit, but the output file still have 2 sub-bricks and cannot be recognized by spm and mricron.
Thanks!
Jinsong
by
jtang
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AFNI Message Board
Hi Cameron,
Thank you so much for your help. My data is preprocessed using afni (-block despike tshift align tlrc volreg blur mask regress ). Do I need to smooth the input data before calculating DC and LFCD? if not I need to rerun the preprocessing without blur option.
Best regards,
Jinsong
by
jtang
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AFNI Message Board
Dear all,
I want to use 3dDegreeCentrality and 3dLFCD method to analysis my data. But there are many options. It is hard for me to choose the best parameters. Does any one have some example codes to run 3dDegreeCentrality and 3dLFCD?
Thank you so much!
by
jtang
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AFNI Message Board