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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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Hi Rick,
Thanks for your information. I will update the AFNI package.
-- Nan
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Nan
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AFNI Message Board
Thanks, Daniel! I found the problem. The scanning plans for the two scans were not identical. This could be the mistake by the scanning technician.
BTW, I think I found a bug in 3dinfo.
When I run "3dinfo -extent FILE1" and "3dinfo -extent FILE2", it shows the extent information correctly; when I run "3dinfo -extent FILE1 FILE2", it shows the extent information f
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Nan
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AFNI Message Board
Hello,
I got a warning message when I used 3dmaskave as below:
=========
Input dataset func_s1_right_decon14+orig grid mismatch from mask.
Try the following command for grid comparison:
3dinfo -header_line -prefix -same_all_grid ./ROI_put_R+orig.HEAD ./func_s1_right_decon14+orig.HEAD
=========
However, I ran the 3dinfo shown above and found that the grid information of the two data se
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Nan
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AFNI Message Board
Hi Gang,
Thanks very much for your help.
I will do more test to confirm the validity of the command 3dTfitter.
Nan
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Nan
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AFNI Message Board
Hi, Gang
Thanks for your help.
As I mentioned before, I am considering to do the PPI analysis. I am wondering how to do the PPI processing without using 3dTfitter if it's not recommended.
Bests,
Nan
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Nan
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AFNI Message Board
Hi Gang,
Thank you very much for your reply.
Let me confirm your comments. So you mean that the reason might be that the regressors in my 3dDeconvolve model are not fully independent with each other. Especially, the regressor -stim_times_IM 7 and regressors of -stim_times_AM1 8~11 are at some extent correlated. That's indeed possible in my regression model.
Acc
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Nan
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AFNI Message Board
Hi Experts,
I would like to inquire about the basic concept of the command 3dTfitter.
According to the help information of the command, 3dTfitter could be used in PPI analysis in the step of estimating the neuronal responses with the BOLD signal of the brain region. The basic algorithm is a de-convolution process. To get a better understanding on the command's function, I did
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Nan
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AFNI Message Board
Dear Jonathan,
I downloaded the updated source code of 3dsvm and compiled it to binary file.
Then I ran the command on my test data for 100 times in sequential way, and checked if the output pname files were identical or not.
Since in my test data there were 3 conditions to classify, the command generated pname files for overall prediction values for all the thre
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Nan
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AFNI Message Board
Hi Jonathan,
I have another question about 3dsvm.
There is an option in prediction/test mode "-nodetrend". Its function is to linearly de-trend the pname file. My question is at what situation the de-trend process is necessary?
Thanks.
Nan
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Nan
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AFNI Message Board
Hi Jonathan,
Thank you very much for your help.
I will try your command and let you know the result.
Bests,
Nan
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Nan
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AFNI Message Board
Hi Jonathan,
Thanks for your reply.
Since I could not wait for the reply to this thread, I modified the source code by myself.
Anyway, I will test your command together with my own and check their output.
One more problem, I think it's more severe.
When I use the prediction mode of 3dsvm, I found that the command can not reproduce previous prediction file (pname file). Below is
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Nan
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AFNI Message Board
Hi all,
I am recently using 3dsvm to analyze my data, and wondering if there is any method to prohibit the program to output the model file in the training mode.
Below is my situation.
My general aim is to find a subregion of ROI which includes the most representative voxels in the decoding algorithm
The basic method is:
1) run linear svm analysis on t
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Nan
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AFNI Message Board
Thanks a lot Rick! It works now.
So what's the difference in the binary package between the intel version and local version? I downloaded and installed the intel version from the afni website previously.
Nan
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Nan
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AFNI Message Board
Dear Experts,
I have got an error message on the library setting after installing AFNI in the Mac OS 10.11.
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
It comes from the command 3dAllineate and 3dClustsim.
I checked previous post, and tried to set the variable of DYLD_FALLBACK_LIBRARY_PATH to AFNI's folder, but still I get the same mes
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Nan
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AFNI Message Board