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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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Pages: 12
Results 1 - 30 of 32
Hi Paul,
Sorry for not provide the system info, the OS is ubuntu 16.04 and afni version is Version AFNI_20.1.07. I just updated afni last month, and the weirdest thing is all the other short cut like ctrl+R or alt+r could work, except the ctrl+r. I can save images in a different way by tapping shift+r, meaning that turn on the recording mode first, and save the current screen shot image next.
by
jack123
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AFNI Message Board
Hi AFNI experts,
Having been using SUMA for plotting for a while, but i still not sure how to save the current view to a jpg file. I know the shortcut key like ctrl+r or ctrl+R, but it just fail for many times. Furthermore, the message when i enter ctrl+r as follows:
++ Notice SUMA_R_Key (SUMA_input.c:2445 @14:06:30):
Oversampling now set to 1
Not sure what is wrong, thanks a lot
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jack123
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AFNI Message Board
Hi rick,
Thanks for your reply. Indeed, the reason that i wanna add "NTRP" is to assure the intactness of temporal structrure, so i can using slidding-window method to analysis dynamic fc, i am not sure it is still work when some of the time points is censered to zero or even 'killed'.
-Jack
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jack123
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AFNI Message Board
Dear AFNI expert,
I wanna try dynamic functional connectivity analysis on rs-fMRI data, but i realise that the censoring step will influence the intactness of temporal structure. So i thought interpolation could be a good choice for the vacant value of censored volumes, but i found that afni_proc.py did not provide aan alternative choice to specify the "CENMODE" which default is supp
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jack123
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AFNI Message Board
Dear AFNI experts,
As far as i konw, there is an option named "-cenmode mode" of 3dTproject. Actually, i need "NTRP" mode to finish the analysis. However, i did not find the same option on the help page of afni_proc.py. So i wonder if not i should run further step by myself to regress out noise after afni_proc.py?
-Jack
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jack123
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AFNI Message Board
Hi,
I wanna make sure that the impact of removing global mean signal from epi time series, but i can not find any option in the afni_proc.py. So I am wondering that if there is possible to remove global mean signal by the relevant options of afni_proc.py, or other afni command to make this happen. Thanks for your attention!
Jack
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jack123
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AFNI Message Board
Hi Rick,
Thanks for your advice, I will check the data step by step.
--Jack
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jack123
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AFNI Message Board
Hi,
Thanks for your attention. As for the max displacement, it is not larger than 3, which is the resolution of voxels. And this dataset got 240 time points in total, but it had been censored out above half time points.
--Jack
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jack123
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AFNI Message Board
Hi,
Thanks for your reply. In this case, I did not add censor_outliers option, so it could be sure that they are censored out by head motion.
--Jack
by
jack123
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AFNI Message Board
Hi AFNI experts,
I am using afni_proc.py program to do pre-processing steps on fmri resting data in anesthesia state, and i found that one of the data is excluded because of censoring too many time points, but after checking 6-d head motion curves by 1d_plot, it is showed as follow, this participant in anesthesia state did not have motion larger than one voxel. I thought it is causing by breat
by
jack123
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AFNI Message Board
Hi, everyone
I meet a problem when I try to transfer .hdr files to nifti files. In my data, 240 hdr files are included in each subject. Then I try to use 3dcopy to thansfer them together , but failed.
FATAL ERROR: 3dcopy only takes one input AND one output filename after options.
So, Is there any body could tell me that how can I thansfer all these hdr files to one nifti fi
by
jack123
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AFNI Message Board
Hi AFNI experts,
I tried to transform data type using 3dAFNItoNIFI, but i got in trouble with the warning message "If you are performing spatial transformations on an oblique dset..". The afni data type(HEAD+BRIK) shows like top figure, it aligned well, but after changing the data type to nifti, it is not that good as shown at bottom figure. Could anyone give me some suggestion?
by
jack123
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AFNI Message Board
Hi AFNI experts,
I got a question here, after i finished preprocessing step by using afni_proc.py, i found some of the data get an error message like:
** ERROR: *** Censoring has made regression impossible :( ***
** FATAL ERROR: 3dDeconvolve dies: Insufficient data (112) for estimating 142 parameters
and my afni_proc.py script as follows:
afni_proc.py -subj_id ${line}
by
jack123
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AFNI Message Board
Thanks for your advise again. This is a detail I never focus before, and I remove the space between '-' and '1'.
However, the same error happened again.
Error: Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct.
Items as follows
-num_glt 6 \
-gltLabel 1 contrast_Time0 -gltCode
by
jack123
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AFNI Message Board
Thanks for your reply. Time' for the number of is basis functions with CSPLINzero following what you said.
However, accoding to your advise, I use glt, there is still an error I met before.
Error:
Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct.
The new script as follows:
#! /bin/bash
3dMVM -prefix ./group_result/name_result/task1_
by
jack123
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AFNI Message Board
Hi Teacher Chen,
The question that we asked you when you were in China has still bothered me.
I have 2 within-subject variables , name(self,other) and Time, 17 subjects. I want to get the effect of self - other on the basis of 6 time points.
Then I ran 3dMVM, but got this ERROR
Error: $ operator is invalid for atomic vectors.
I am confused because there is no any $ in my script
by
jack123
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AFNI Message Board
Hi,
I try to do the detrending step by command 3dDetrend with polort 3 on rs-FMRI data , but i found that the max displacement of head motion became much more bigger, so does it have specific order to do this, i.e, do the detrending after head motion correction?
by
jack123
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AFNI Message Board
Dear afni experts,
After doing the step of hierarchical clustering, i try to read the nifti files by AFNI, but there is an error message:
** AFNI can't handle NIFTI datatype=1024 (INT64) in file /home/jack/Desktop/ward_parcellation2.nii.gz
I tried to search by google it but did not get any solution, so i hope you guys could tell me how to solve it, thanks a lot!
--Jac
by
jack123
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AFNI Message Board
Dear afni experts,
I wonder that if afni could do the hierarchical cluster to get a specified number of rois. The reason i wanna do this is i wanna do power-law fit using degree centrality data, i tried each voxel value(correlation coefficient, threshold > 0.3 ) in the whole brain by using 3dmaskdump, but the result does not seem good.So i wanna try it in this way.I hope to get your ans
by
jack123
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AFNI Message Board
Hello anfi experts,
i have been doing the data analysis these days,but i found that there is a sentence on the print read that " WARNING: file /home/jack/.afni.log is now 605662936 (606 million ) bytes long!",i am not sure if it will influence the processing.
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jack123
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AFNI Message Board
Mr. Chen
The model is TENTzero.Should i average them all to put the result to 3dANOVA3?
-Jack
by
jack123
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AFNI Message Board
Mr. Chen,
Sorry i didn't offer enough information, the experiment is a event-related design, and it has three sessions, including consciousness,sedation and unconsciousness,and for each session has 60 trials,30 trails for calling the own names of the subjects,30 trails for calling unknown names of the subjects.The 10 β values i mentioned before are from the result of 3dDeconvolve.I though
by
jack123
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AFNI Message Board
Dear AFNI experts,
I tried to do group analysis by using the command 3dANOVA3,but the result didn't seem good.So i am wondering that is there some problem about the analysis for every single subject? After preprocessing, i analysed the data by 3dDeconvolve and got the results .Cause it has two different kind trials of the data,so i get the β values by using 3dTcat, and then average t
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jack123
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AFNI Message Board
Mr. Chen
okay,thanks a lot. I am going to try it right now.
-Jack
by
jack123
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AFNI Message Board
Dear AFNI experts
I am just trying to use the command "3dMVM" in AFNI to do the group analysis,but i don't know how to write the code by reading the examples on ur page.And i really need ur help to finish it.
The data i get here has 3 sessions for each subject , that is in the state of consciousness,sedation and unconsciousness.And the tasks for each session is calling the ow
by
jack123
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AFNI Message Board
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