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Re: A naive question - 13 days ago
Thanks Rick and Gang. Yes. I am planning to treat fMRI as resting state data. I would like the data to be free of motion,trend and any other nuisance effects. I prefer to use afni_proc.py but i can write my own code if necessary. I will check out the examples and see if the -errts is what I needed. I assume that the -errts would be demeaned as well?by TJIANG - AFNI Message Board
A naive question - 13 days ago
if i just want to preprocess the fMRI data without explicitly modelling the data (i am not interested in the GLM etc.. ). is there any options to do that. that is to say, i just want to do slice time correction, motion correction, trend removal and smoothing. I noticed that the polynomial trend is removed on the fly (it is modelled in the GLM) . is there a way to get the residual fMRI time coursby TJIANG - AFNI Message Board
Re: Data distributed with AFNI - 26 days ago
great,I will give it a try. Thanks a lot!by TJIANG - AFNI Message Board
Re: Data distributed with AFNI - 26 days ago
Hi, Rick well, what I am trying to do is to do a deconvolution analysis on one of my old fMRI dataset. It has two different type of motor tasks A and B . In each task block (10TR) , it starts with 1TR Cue , 1TR Movement and 8TR REST; the entire paradigm looks like this Initial REST(8TR); A;B;A;B... what I am trying to do is to deconvolve the time series to see if the HRF magnitude differs iby TJIANG - AFNI Message Board
Data distributed with AFNI - 26 days ago
I am reading the AFNI_DOC and somewhere it mentioned using a dataset called V2:time+orig and Monica+orig. anyone has any idea where I can find the data? Thanks. Tonyby TJIANG - AFNI Message Board
align_epi_anat.py failed but flirt worked - 5 weeks ago
have spent the afternoon trying to figure out why. tried many options thought this might be caused by deoblique but it wasn't the obliquity. I have uploaded the data (anat+orig and epi+orig). appreciate if someone can look into this and possibly point me what I did wrong. the script I used align_epi_anat.py -epi epi+orig -anat anat+orig -epi2anat -giant_move -epi_base 0 (i have tried with andby TJIANG - AFNI Message Board
Re: deoblique in same session - 5 weeks ago
update: Ok , I understand why the deobliqued dataset looks different when viewed in AFNI. AFNI viewer doesn't reslice the data. I converted the data to nifty and checked in mricron the before and after deoblique match each other.by TJIANG - AFNI Message Board
deoblique in same session - 5 weeks ago
can someone tell me how exactly this is done? I have an anatomical scan and an EPI. I understand these datasets have different obliquity and I know how to deoblique on each dataset. but not sure how to get them done in same session? Another related question is, when I view the dataset before and after deoblique, they look different? is this expected?by TJIANG - AFNI Message Board
Re: newbie questions - 5 weeks ago
Thanks Glen. I will try that and see how it goes.by TJIANG - AFNI Message Board
newbie questions - 5 weeks ago
Dear all, I have some newbie question. I used to work with SPM and recently decided to give AFNI a try. I have a set of fMRI data and I was wondering how 1) I used simple.sh to process my data. it looks good on its original space. Then I used align_epi_anat.py to register stat results with the anatomical data. But if I overlay on anatomical , I got a warning message of difference in oblique dby TJIANG - AFNI Message Board
3dTfitter help - 11 months ago
So I am trying to regress a .1D file on another .1D file , but the output is actually in .3D ASCII format even I explicitly requested a .1D in -prefix . Based on the help manual of 3dTfitter, i should've seen a true .1D file (only numbers in column formats) --------------- OUTPUT OPTIONS: --------------- -prefix p = Prefix for the output dataset (LHS parameters) filename.by TJIANG - AFNI Message Board
Re: 3dTshift question - 11 months ago
that was fast!! How come I haven't thought of that!! Thanks, Tonyby TJIANG - AFNI Message Board
Re: 3dTshift question - 11 months ago
I guess i have a follow up question. with 3dvolreg, we get to specify the -tshift ii. the manual says this is like running 3dTshift first then a 3dvolreg. my question is, how do we specify which slice to be the reference slice (time 0) ? it doesn't look ii is the parameter (The integer 'ii' is the number of time points at the beginning to ignore in the time shifting. link: )by TJIANG - AFNI Message Board
3dTshift question - 11 months ago
Dear All, This question might sounds naive but I am a beginner to AFNI. I tried to run 3dTShift to do slice time correction and I dont see an option for new output directory. everytime i ran the command, the newly created volumes were save in my working directory. Did I misread the help? or are you guys aware of a way to do this? right nowi have to write a script to manually move it to theby TJIANG - AFNI Message Board
