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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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Results 31 - 46 of 46
Hi AFNI experts,
I am trying RetroTS.m to get the regressors for physiological correction.The original files(format: xxx.resp) of physiological noise were acquired via a Siemens 7t scanner. And files (in .txt format) with raw numbers were generated by removing words of head information in .resp files. And now I need to know what should the data be to be inputted to RetroTS:
1) The raw numbers (
by
Zhang Yu
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AFNI Message Board
Hi all,
I want to figure out the casual relationship among three brain regions and DCM is widely known to solve this problem. Does AFNI have a way to calculate DCM or some alternative methods? Do I have to transform the .brick + .head format to a format that SPM can read ?
Thank you!
Yu
by
Zhang Yu
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AFNI Message Board
Hi ,
The values of Coef, Tstat, Fstat and R^2 of each condition can be outputted by 3dDeconvolve after regression analysis. P values of these statistics can also be displayed at the bottom of the AFNI GUI when the bricks of Tstat, Fstat or R^2 are chosen as the Thr (threshold). But I really want to know where the p values are stored in the datasets now that the p values are not stored as an i
by
Zhang Yu
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AFNI Message Board
Hi AFNI experts,
There are two problems about gen_epi_review.py and @ss_review_basic at the end of preprocessing each time I run the standard preprocessing
script which is generated by uber_subject.py , no matter whether I use the administrator account or not. The outputs in the terminal window are:
...
gen_epi_review.py -script @epi_review.FT -dsets pb00.FT.r01.tcat+orig.HEAD pb0
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thank you!
The version number seems to be normal. But the date outputted by 'afni -ver' is 'Aug 7 2009 ' while this output was 'January 11 2016' before updating. And the time (2009-08-07 14:59:02.000000000 +0800) of last change outputted by 'stat align_epi_anat.py' is weird.
by
Zhang Yu
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AFNI Message Board
Hi,
I decided to update my AFNI because I was told there were some good updates in the latest version. I checked my version before updating and the version on my machine seemed to be 'January 11 2016(...)'. I can't remember the number in the bracket now. Then I executed the command ' @update.afni.binaries -defaults'. It took some time. I checked the version using '
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thanks a lot for your answers! The original EPI contains only a part of the brain because we wanted to increase the spatial resolution of our ROI in the process of collecting data.
But now I would like to know whether the -partial_* option is essential for alignment. Because the preprocess using uber_subject.py has already taken too much time and the alignment without the opt
by
Zhang Yu
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AFNI Message Board
Hi,
I used to preprocess the functional images of the whole brain using uber_subject.py. But the functional images I got this time contain only a middle part of the brain. Do I need some extra operations besides the preprocessing steps given by uber_subject? How to align EPI of only a part of brain to anatomy images ?
Thank you!
Yu
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thanks for your answers !
I have ROIs of the whole SC now. But I have no FreeSurfer surfaces and I want to finish creating ROIs of different depth in a short time.
So the solutions I can find are :
1.Draw the first layer (the surface layer or the 0 mm layer) of the SC ROI manually.
2.Calculate the shortest distance from the other voxels in the ROI of the whole SC to a
by
Zhang Yu
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AFNI Message Board
Hi all,
I want to divide the superior colliculus (SC) into different layers according to the physical distance from each voxel in SC to the surface.That is,I want to make ROIs of different depth from the surface of the SC.The depth for each voxel in the SC will be calculated as the shortest distance from the voxel to all surface voxels.I would like to know if there are some other ways to make
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thanks a lot!
Why F-stats correspond with 2-sided thresholding (what's the thresholding method of 3dclustSim?)?
How to set 3dclustSim to work specifically for F-states using 2-sided thresholding?
When I saw image data in GUI,I just found "bi-sided" could be chosen after pressing "*Clusterize" button.But there seemed to be no difference between the result
by
Zhang Yu
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AFNI Message Board
Hi,
The 3dclustSim generates several random brain volumes and calculates different degree (namely p-value) between distinct experimental conditions of these brain volumes. Then counts the probability of forming clusters of specific voxel number in these random volumes.
If the former paragraph is right,which kind of p-value calculated from the random brain volumes will affect the results.
by
Zhang Yu
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AFNI Message Board
Hi Daniel,
Thanks a lot!
The ROI I need to draw is the smaller posterior insula and I had planned to use the atlas provided by AFNI to draw . But only a region named 'left(right) insula' was included in TT_Daemon atlas.And the larger anterior part of insula is not interested.I don't want to draw ROI manually because I am not familiar with the position of posterior insula .
Do
by
Zhang Yu
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AFNI Message Board
Hi,
I found the regions included in an atlas can't all be displayed in the 'Choose Atlas' list of the Draw ROI plugin .So I need to know how to change the displaying way of 'Choose Atlas' list and enable this list to display all the regions included in TT_Daemon? And how to see all the brain regions included in an atlas using afni code? Whereami or some functions else
by
Zhang Yu
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AFNI Message Board
Hi,
I am sorry for the unclear statements. I didn't receive expected results in the voxel-by-voxel group analysis. I am interested in posterior insula, but I didn't conduct the experiment of functional localizing. Besides drawing an ROI of global posterior insula,I want to draw large number of spheres in posterior insula and compare different conditions sphere-by-sphere. So I nee
by
Zhang Yu
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AFNI Message Board
Hi,
I want to draw ROI using coordinates of every voxel included in insular as the center. So I need to get the coordinates firstly.How to get the coordinates of all the voxels included in insula using codes ?
Thank you!
by
Zhang Yu
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AFNI Message Board
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