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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
Page 3 of 3
Pages: 123
Results 61 - 83 of 83
I can't find a way to set up individual modulation via the AFNI proc. Is this something that I simply have to write into the tcsh myself?
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s1110a
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AFNI Message Board
Thanks for the suggestion, I can try this but could my issue simply be a problem with the label? Maybe it is still in MNI but it has been labelled TLRC. How could it go from one space to another without a transform being applied to it? Are there any other methods of testing which template space it is in?
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s1110a
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AFNI Message Board
Thanks for your response,
3dinfo -space -av_space for my errts file gives me
TLRC +tlrc errts.s1.tproject
I forgot to mention that I had to make some changes to my tcsh script. Between the mask making stage and the blurring stage I inserted a stage that calls on matlab code the implements CompCor. The output is then plugged into the blurring stage. The only other chan
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s1110a
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AFNI Message Board
afni_proc.py \
-subj_id s${subject} \
-script proc.Rests${subject}.tcsh \
-dsets s${subject}/func/orig/REST.nii \
-copy_anat s${subject}/anat/orig/t1_MPRAGE.nii \
-blocks despike align tlrc volreg mask blur regress \
-volreg_align_to third
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s1110a
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AFNI Message Board
Thanks
This is good but small is ralative and I have no frame of reference so what is small in this case? When it comes to the 288 values they are for my RT values. I hope that I placed those values into my timing flies correctly (onset*Centered RT). I am aware that AFNI centers for you but it centers to a global mean (across runs). I wanted each block(run) centered to the RT mean for that
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s1110a
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AFNI Message Board
I posted the output I got after running 3dTstat (3dTstat -max -prefix - X.xmat.1D\') I am not sure what is happening with the "assuming TR=1.0" this worries me.
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
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s1110a
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AFNI Message Board
Thanks for your help. I am running 3dDeconvolve with the new time files created by using -round times. What is an inter-knot TR?
I get this message *+ WARNING: -stim_times_AM2 1 .. TENT(-7.7,15.4,34) has inter-knot TR=0.7 but -iresp output TR=0.7
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s1110a
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AFNI Message Board
Below I pasted the contents of the file you mentioned for one of my subjects. It seems like I have small offsets so I am almost TR locked. Considering that this can impact the value of beta#0 this is probably the culprit but when it comes to TENT are there certain preprocessing steps I should worry about? For example I censored some excessive motion TRs and I wonder if this could be problemat
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s1110a
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AFNI Message Board
I will look into this although I don't this is the problem. All of my events were synchronized with the scanner (linked to a TR signal). Granted the actual stimulus events had hard coded duriations since the desired times were not divisible by the TR. A buffer zone event was placed after the stimulus events in order to get things back in sync. The ITI that preceded the stimulus was TR li
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s1110a
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AFNI Message Board
I used afni_proc.py. I did not see a timing warning but I take another look. Things look pretty booked up today so I will take a look at the timing tool tomorrow and I will get back to you.
Thanks
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s1110a
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AFNI Message Board
When I run 3dDeconvolve with the TENT function my first coeff is always an outlier. I don’t think this is a real reflection of my data considering that the outlier time point (note: my tents are now TR locked) changes depending upon where my window starts. I originally was using TENT (0,15.4,23) and the first coeff (the one I believe is associated with the onset) was the outlier. I then ran 3d
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s1110a
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AFNI Message Board
Okay so it is the start point of the final TR. I was thinking it would be listed as the point when the last TR completed.
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s1110a
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AFNI Message Board
A mistake in one of my timing files lead to a PSFB Syndrome issue "range 0 .. 366.1 ". The timing file issue has been corrected but the PSFB Syndrome might have brought another issue to light. 366.1 is not correct and the range should extend to 366.8 s. My TR is .7 s and I have 524 TRs. I checked my nii files and they state the correct number of TRs. Where in my pipeline might have
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s1110a
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AFNI Message Board
I was not aware of this when I formatted my timing files but it seems like AFNI will center my auxiliary data (RT) for me. I have centered my RT's to the mean for each run. Before I stop centering my data myself and let AFNI handle that job I would like to know if AFNI centers to the run mean or the grand mean (across runs). What mean does AFNI use? It seems like I will have to chang
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s1110a
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AFNI Message Board
Yeah that was really stupid on my part. I thought of that not long before reading your response. Since my the coeffs for my auxiliary predictor did not show up in the iresp I will rerun 3dDeconvolve with TENT(0,15.4,23).
Super thanks
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s1110a
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AFNI Message Board
Thanks a lot for your help and in regards to D. that makes total sense
3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 \
-local_times \
-num_stimts 8
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s1110a
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AFNI Message Board
Tent to PSC
Background (2 conditions 22 TR locked estimates/additional 22 RT auxiliary parameter estimates for each condition)
A.
I have a few questions in regards to the issue of PSC with Tent functions. To put it simply I want to get ((target-baseline)/baseline)*100) for each of my time points covered by my tent function. I have 3 trend terms (linear, quadratic, cubic) and I was wonderin
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s1110a
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AFNI Message Board
I am fairly new to fMRI research and I am in the process of trying to make use of a tent function for the first time. I have two trial types denoted as flcond & flincd. My objective is to get estimates for 22 time points (a 15.4 sec period, 700ms TR) starting at the stimulus onset for each trial type in addition to RT auxiliary parameters.
# run the regression analysis
3dDeconvolve
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s1110a
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AFNI Message Board
Page 3 of 3
Pages: 123