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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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I misunderstood that the set of ROIs input can be input individually. It worked well now. Thanks for the very useful information.
-Hema
by
hemasam
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AFNI Message Board
Hi Rick,
Thanks for the suggestions and help! It was very helpful.
-Hema
by
hemasam
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AFNI Message Board
I'm working on implementing the method you suggested, as shown below:
#First, we need to extract the ROI time series data from the 3dDeconvolve errts output to a text file.
3dmaskave -mask ../masks/lAmygdala_roi+tlrc. -mrange 33 33 -quiet errts.$subj.tproject+tlrc. > ${subj}_lAmygdala.1D
3dmaskave -mask ../masks/rAmygdala_roi+tlrc. -mrange 34 34 -quiet errts.$subj.tproject+tlrc
by
hemasam
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AFNI Message Board
Thanks for letting me know this interesting function. Its a new function. I gave it a try and ended up with the following error.
3dNetCorr -inset errts.A0105.tproject+tlrc. -in_rois ../masks/lAmygdala_roi+tlrc. ../masks/rAmygdala_roi+tlrc. -fish_z -ts_wb+corr -mask mask_anat.A0105+tlrc. -prefix A0105.Amy.corr
++ Reading in.
++ Allocating...
++ Labelling regions internally.
++ Getting volu
by
hemasam
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AFNI Message Board
Seed time series are generated using ROI's. Thanks for the suggested method. How about 3dTcorrelate function? Does the input have to be entire volume? I was wondering if it will work with the ROI's time series pairs?
Thanks
Hema
by
hemasam
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AFNI Message Board
Yes, I meant about the errts file being zero for the censored TRs. I appreciate your help, thank you!
Could you also please give a lead as how to do connectivity analysis between two seed regions?
-Hema
by
hemasam
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AFNI Message Board
Dear AFNI experts,
How can I do connectivity analysis between two ROI's (left dorsal ACC vs right dorsal ACC)? Will 3dGroupInCorr help or is there other ways to do it?
Thanks
Hema
by
hemasam
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AFNI Message Board
Hi Rick,
Hope you had a chance to look at my data. I'm waiting to hear from you.
Thanks
Hema
by
hemasam
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AFNI Message Board
Hi Rick,
It was very useful and worked well! I noticed couple of issues, the errts file created through the afni_proc.py script is empty for few subjects (no errors or warnings) and there is no stats output file for any subject. Even though, we need the errts output for connectivity analysis, I would like to know the reason for the failure to make stats output data. Could you please help to so
by
hemasam
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AFNI Message Board
Dear AFNI gurus,
I'm running preprocessing for resting state functional connectivitiy using the afni_proc.py example 9a. The problem is losing quite a few subjects because of bandpass filtering and censoring as a result of motion. I changed censor options to -regress_censor_motion 0.3 -regress_censor_outliers 0.5, but still they fail as there not enough degrees of freedom.
I would like
by
hemasam
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AFNI Message Board
Hi Rick,
Its a little confusing. I did use the afni_proc.py from the afni version I mentioned to you. It generated 3dDeconvolve, instead of 3dTproject. Then should I update afni?
Thanks
Hema
by
hemasam
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AFNI Message Board
Hi Rick,
The script finished running friday evening. I did notice that during 3dDeconvolve, the num_stimts extended from 6 to 288 due to -ortvec, which suggested that it would be bandpass filtering slowing down.
The afni version is:
Version AFNI_2011_12_21_1014
[]
The final stats output of the process is completely zero, which is strange. I'm as well attaching the 3dinfo of the
by
hemasam
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AFNI Message Board
Dear AFNI team,
I am using afni_proc.py script to do resting state analysis. I chose mostly the default options for the RS analysis and the issue is with the 3dDeconvolve process. Its been more than an hour since I executed the script and its still entering voxel loop in the 3dDeconvolve operation. I'm unable to figure out the cause for it. Please help
I'm attaching the script as
by
hemasam
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AFNI Message Board
We have a project analysed in SPM and the contrasts of the within subject (ws) factor is available as .hdr/.img files. We would like to see the effect of the ws factor on all normal controls with depression measure as covariate. Hence, I did 3dttest++ on the controls using depression scale as covariate. With the ttest++ map thresholded for p=0.0014 with 20 voxels (not corrected), I pull out the m
by
hemasam
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AFNI Message Board
Dear AFNI gurus,
Is there a way to draw a cube ROI given the six parameters - pitch, roll, yaw,x, y,z in afni? Our primary goal is to able to have a perfect cubical ROI.
Thanks
Hema
by
hemasam
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AFNI Message Board