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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
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Hi rick,
Thanks, I'll give this a shot!
Yes, I do see the warnings now. See attached image.
-Heather
by
heatherb
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AFNI Message Board
This seems like the culprit. Here's the output:
timing_tool.py -multi_timing stimuli/*tent.txt -tr 2.0 -warn_tr_stats
within-TR stimulus offset statistics (stimuli/sub104_imagine_amb_norming_tent.txt) :
per run
------------------------------
offset means 0.009 0.009 0.007
offset stdevs 0.002 0.003
by
heatherb
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AFNI Message Board
Hello,
I am trying to use the TENT function to run an FIR analysis. I did this using afni_proc:
afni_proc.py -subj_id s$sub \
-script proc.s$sub.3conds_norming_tent \
-out_dir s$sub.3conds_norming_tent.results \
-dsets func/sub-s${sub}_ses-01_task-combo_run-0*_bold.nii.gz \
-copy_anat anat/anatSS.s${sub}.nii \
-anat_has_skull no \
-blocks tshift align volreg mask blur sc
by
heatherb
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AFNI Message Board
Hi,
I'm trying to interpret the output of my 3dlme output and hoping someone might be able to lend a hand. I ran two similar versions of the same script, changing only the glt contrast coding.
Here's MODEL 1:
3dLME -prefix corr_group_lme -jobs 18 \
-mask MNI_re+tlrc \
-model 1 \
-ranEff '~1' \
-num_glt 2 \
-gltLabel 1 'UNVAMvsAMB' -gltCode 1 'c
by
heatherb
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AFNI Message Board
In case it helps you or anyone in the future, I just worked on this question myself and this seemed to have worked for me:
I ran @SSwarper to transfer my native space anat into MNI. This outputs a .1D file with the warping info. From there I just ran these two lines:
invert the warp so it is MNI>native:
cat_matvec -ONELINE anatQQ.s${sub}.aff12.1D -I>warp_Matrix.1D
apply the inver
by
heatherb
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AFNI Message Board
Hello,
I am trying to do a univariate contrast with three runs of data, but the TR length of my first run (2.25 s) differs from the TR length of the second and third runs (2.8 s). Is it possible to do this with 3ddeconvolve? I just ran my analysis as follows:
3dDeconvolve -input functional_loc_ns+orig.HEAD functional_enc_r02_ns+orig.HEAD functional_enc_r03_ns+orig.HEAD -polort A \
-nu
by
heatherb
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AFNI Message Board
Hello!
I have been working for a while now trying to get cluster thresholds by using 3dClustSim for a 3dLME group analysis I ran, but the thresholds I am getting still seem strangely low. For a wholebrain with functional data smoothed at 6 with 3dBlurToFWHM, at p threshold of .005, alpha of .05, NN2, bi-sided, it recommends a threshold of 16.3 (voxel size 3.125 mm x 3.125 mm x 3.125 mm). I am
by
heatherb
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AFNI Message Board
Ok, thank you!
One last question! In a separate set of analyses, we will want to keep data for the whole run in the model (meaning we will not be estimating each trial separately). In this instance, I believe it is the case that we should use dmBLOCK. Could you clarify which stim_times variant would be appropriate in this case? This is with the same dataset, so trial durations are equal t
by
heatherb
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AFNI Message Board
Yes, that is correct. We do this before conducting mvpa analyses for rapid event-related designs.
Ok, if I do not want to modulate each trial in the model, then would you recommend that I use dmBLOCK with a simple stim_times option (no AM1 or AM2)? The documentation online stated, "If different stimuli in the same class 'k' have different durations, you'll have to use t
by
heatherb
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AFNI Message Board
Oh, I realized I never mentioned that the trial duration is the reaction time for the trial, which is why it feels redundant. Sorry about that!
by
heatherb
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AFNI Message Board
Hello
I have a rapid event-related design and the duration of my trials are variable. My plan is to run 3ddeconvolve on each individual trial so I can run MVPA. As I was reading over the 3ddeconvolve options, it seemed to me that the recommended options would be to use 'dmUBLOCK(1)' with -stim_times_AM2. My confusion is simple (I hope). I don't really understand what I am m
by
heatherb
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AFNI Message Board
Hello!
I am trying to do a basic contrast between conditions during a localizer run and am having some issues. I originally ran the following 3ddeconvolve line where my input file was preprocessed to pb03. After, I didn't find many significant clusters, so I thought I would try with a pb05 input file. I ended up finding (for multiple subjects) that my two GLT contrasts were producing t
by
heatherb
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AFNI Message Board