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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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Dear AFNI experts,
I am sure it is possible, but I can not find a solution: how can I use my own brain mask (preferably '.nii', or '.nii.gz') in afni_proc.py? so that the analysis runs only within the mask and I do not calculate the brain mask via AFNI. Is it somehow related to '-mask_import'?
Sorry for bothering you!
Best regards,
Wiktor Olszowy
by
wo222
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AFNI Message Board
Dear Gang,
Thanks a lot for your response! So it looks like this is only a numerical issue. However, adding option "-datum float" to 3dcalc did not change the results. "3dmerge -1zscore" sounds like a very helpful command, but actually for my AFNI-format data it only works for the t-statistic map (brick [2]), not for the F-statistic map (brick [0]):
3dmerge -1zscore st
by
wo222
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AFNI Message Board
Dear AFNI experts,
I am transforming F- and t-statistic maps to z-statistic maps using 3dcalc. In some cases (when df1=1) I think that the z-statistic map resulting from the transformation of the F-statistic should be the same as the z-statistic map resulting from the transformation of the t-statistic. However, I tend to get slightly different results in such cases. I am wondering if this is d
by
wo222
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AFNI Message Board
Dear Peter,
Thanks a lot for your response! Indeed, the problem was with the header (for the datasets with resulting +tlrc files, the headers also had wrong TR, which is why I used '-force_TR'). I did not think that AFNI checks the space code from header (using sform_code?) and then changes the output file names accordingly, but actually it makes sense. Regarding '-volreg_tlrc_w
by
wo222
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AFNI Message Board
Dear AFNI experts,
I am using the same code for different datasets and for some datasets the results are in original space (files have the +orig extension), while for some datasets the results seem to be in Talairach space (there are the +tlrc extensions). I am using AFNI 16.2.02 and the code is:
afni_proc.py \
by
wo222
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AFNI Message Board
Dear Rick,
Thanks a lot for your response! I understand that putting duration times twice for AM1 is not a problem, once in the timing file, once in -regress_basis 'SPMG2(20)', is it? I have already analyzed the data, would have to re-analyze, and my results make sense: there is a lot of significant activation in the visual cortex and the stimulus was visual. So I presume the duratio
by
wo222
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AFNI Message Board
Dear Rick,
Thank you so much for the response! Answering your question, the timing file is:
20:20 60:20 100:20
I am wondering what is the advantage of AM2 compared to AM1 if the duration times are the same (as it is in my example)? if I understand page 16 in the class handout you mentioned, the additional regressor will just be a constant. Maybe that causes the numerical problems? The GL
by
wo222
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AFNI Message Board
Dear Rick,
Thanks a lot for your response! Regarding the use of 3dinfo, I was looking at single bricks using the square brackets, but it is indeed more convenient to use the -verb flag to see all of the information together. Thanks for the suggestion! Regarding GLT, I deleted the 4 lines:
-regress_opts_3dD \
-jobs 1 \
-gltsym 'SYM: activation_stimulus' \
-glt_label 1 activit
by
wo222
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AFNI Message Board
Dear AFNI experts,
Two weeks ago I struggled to export the t-statistic map after a single subject analysis. I asked a question on the message board, did not get any help, but was later able to solve most of the problems by myself:
However, I still do not understand why two bricks in the 'stats_REML' output are so similar to each other, and which one is the t-statistic map for
by
wo222
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AFNI Message Board
Well, now I know that '3dinfo' provides more information about the 'stats.${subject}_REML+orig' images/bricks than its AFNI header. Thus, I see that some bricks are coefficient maps rather than statistic maps. Yesterday I was thinking that all 9 bricks in my 'stats.${subject}_REML+orig' are F- and t- statistic maps, some of which referred to the motion covariates...
by
wo222
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AFNI Message Board
In the search for a t/z statistic map, I was looking for an image with high values in the visual cortex, as the experiment was with a visual stimulus: boxcar 20s off + 20s on. After checking today 'sum_ideal.1D' I realised that 3dDeconvolve did not convolve SPMG2 with the stimulus duration times, and that is why the fits were poor and nothing in the 'stats.${subject}_REML+orig'
by
wo222
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AFNI Message Board
Dear AFNI experts,
I am new to AFNI and struggle to figure out where the statistic map is saved after running afni_proc.py without multiple testing. Is it one of the images within stats.${subject}_REML? I run afni_proc.py with the following options (canonical HRF with derivative):
afni_proc.py \
-subj_id $subject
by
wo222
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AFNI Message Board
Dear Rick,
Thanks again for your response! Switching pnum to 2 effectively switches polort off, does it not? What are the reasons you do not suggest removing signal corresponding to low frequencies, e.g. <1/100 Hz? Sorry for so many questions!
Best,
Wiktor Olszowy
by
wo222
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AFNI Message Board
Dear Rick,
Thanks a lot for your response! Removing only drift at 1/320 Hz might be sensitivity-inefficient. It might be expected that low frequency drifts are either related to the scanner or to the task-unrelated physiology and thus they should be removed. Otherwise, the low frequency drifts decrease the sensitivity for task-fMRI analyses. In FSL and SPM by default all low-frequency drifts b
by
wo222
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AFNI Message Board
Dear AFNI users,
I have very little experience working with AFNI and among others I can not fully understand its high-pass filter. Why is the default cutoff frequency so low? I see in the help:
** For pnum > 2, this type of baseline detrending
is roughly equivalent to a highpass filter
with a cutoff of (p-2)/D Hz
by
wo222
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AFNI Message Board