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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:
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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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Thanks. I've attached the two jpegs from SSWarper here. Will post another with screenshots from the afni_proc.py QC output. It seems like these look pretty good, but the EPI to anat (next post) looks not as good (though not horrible - mainly near cerebellum). Thus my befuddlement.
by
kkerr
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AFNI Message Board
Thanks - I had forgotten about the partial coverage option. Sadly that didn't seem to work, even with trying out the different cost function options. The thing that gets me is that it looks decently aligned in original space; it's only after the Talairach transform gets applied that things seem to go awry. I've attached a screenshot of the aligned EPI and anat in original space (th
by
kkerr
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AFNI Message Board
Thanks. I tried with -multi_cost so I could compare different cost functions. Some are better, but none are great, and -nmi and -lpa actually make the anatomical quite distorted (to use a technical term, it looks squished).
Not sure if this is playing a role whatsoever, but I also looked at the @SSwarper output again, and noticed in the posterior portion of the brain it is not very precise-lo
by
kkerr
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AFNI Message Board
Yes, of course. Details below:
+@SSwarper followed by afni_proc.py (will paste afni_proc.py command below). The issue is with the EPI to anatomical alignment.
+Image attached.
+20.0.19 (I know it's slightly older, but I'm using an analysis cluster and this is the newest available.)
In investigating this issue and another one I'm having with a different participant, I can
by
kkerr
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AFNI Message Board
I noticed some alignment issues with one of my datasets, and I think (though am absolutely unsure) that the issue might be because the bottom-most portion of the cerebellum was cut off in the original acquisition. Aside from that, the original EPI and anatomical datasets line up pretty well, which is why I was surprised to get the misaligned output at the end of preprocessing. Are there any progr
by
kkerr
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AFNI Message Board
Thanks, I tried this, but unfortunately it turned out almost exactly the same. Thinking it may be another issue? Of note, prior to your helpful response on the other thread about using @Align_Centers, I had processed this participant's data in MNI space and had similar problems. Apologies, should've noted that before.
Regarding the pb00 filename, that's just one of those things
by
kkerr
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AFNI Message Board
Hello,
I am having great difficulty in aligning the EPI to the anatomical for one of my participants. In original space, they are aligned quite well, but after warping it comes out off. I've tried numerous different cost functions to no avail. I've attached some screenshots I hope will demonstrate this. These are using the cost function lpc, which thus far seems to result in the best
by
kkerr
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AFNI Message Board
Thank you so much! Just tried this out on a different participant, and it definitely seems to be solving the problem. Thank you for restoring our frontal lobes.
by
kkerr
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AFNI Message Board
Thanks. Would you need just one of the input datasets?
If it is helpful information, I discovered that this error does not occur if the '-mask' option is used.
by
kkerr
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AFNI Message Board
Hello,
I ran @SSwarper on about 30 participants, and most of them (~20) came out with frontal clipping after skull stripping. I tried using "-SSopt '-push_to_edge'" but the clipping still occurred. Any suggestions? Data from these participants had previously been processed the old way with linear warping using 3dSkullStrip from afni_proc.py, and this issue didn't occur
by
kkerr
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AFNI Message Board
I'm having trouble running a 3dMVM script using the robust option. I keep getting the following error:
Error in if (fm$converged) { : argument is of length zero
Calls: aperm -> apply -> FUN
Execution halted
This occurs at various times when I try to run it, sometimes right after reading the input files and sometimes all the way down at Slice 75. Most recently it stopped after
by
kkerr
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AFNI Message Board
Hello,
We are analyzing repeated scans, two for each participant, and we have reason to believe that physiological functioning may have changed between the scans. In short, differences in activity during the task between the two scans are reduced to not meeting the statistical significance threshold when we use RVT and RETROICOR (but are present when we do not include them). We would like to h
by
kkerr
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AFNI Message Board
Hi Gang,
Thanks for your help. I tried the following command:
3drefit -substatpar 0 fico 14 parent_youth_spearman_corr_3dtcorr1d_17dyads+tlrc
But it does not seem to work. The command runs, but when I open the file everything is significant at a p-value of .005 (and I mean everything...). I also tried it with '31' instead of '14' because I wasn't sure if I was s
by
kkerr
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AFNI Message Board
Hello,
I'm attempting to use 3dTcorrelate to obtain Spearman correlation values for the relationship between parents' and children's responses during a task condition. I first used 3dTcat to put each subject's values into sample datasets ('parent_sample_17dyads+tlrc' and 'youth_sample_17dyads+tlrc'). I then ran the following command:
3dTcorrelate -spe
by
kkerr
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AFNI Message Board
Yes, that might be it. One mask is a whole-brain mask, and the other covers most of the brain but does not include ROIs that we are doing small volume corrections for.
by
kkerr
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AFNI Message Board
I've pasted the tables from the three different 3dClustSims we ran below (with the command lines).
Original 3dClustSim with larger mask:
# 3dClustSim -both -mask mask_overlap_youth_27subjs.7+tlrc -acf 0.520152 5.1862 12.4322 -prefix 27youth_ACF_ClustSim.mask_overlap_youth_27subjs.7
# 2-sided thresholding
# Grid: 92x109x86 1.75x1.75x1.75 mm^3 (246932 voxels in mask)
#
# CLUSTER S
by
kkerr
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AFNI Message Board
Hi,
We noticed that running 3dClustSim on two different masks resulted in higher cluster thresholds for the smaller mask (237709 voxels) than the larger one (246932 voxels). The acf values were very similar (they came from the same sample), but just to test it I ran the 3dClustSim command for the smaller mask with the acf values from the larger one, and this lowered the thresholds only a littl
by
kkerr
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AFNI Message Board
I noticed that in 3dMean the help file states that the option -sd (or -stdev) calculates "the standard deviation (variance/n-1)." It is my understanding that in order to get the standard deviation you simply take the square root of the variance, rather than what the help file states, which is divide the variance by n-1. I used 3dcalc to go through the individual steps to calculate the v
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kkerr
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AFNI Message Board
Sure thing.
3dttest++ \
-setA absubjs \
aa610 ranked_unhealthy-healthy_ab+tlrc'[0]' \
aa628 ranked_unhealthy-healthy_ab+tlrc'[1]' \
aa655 ranked_unhealthy-healthy_ab+tlrc'[2]' \
ab043 ranked_unhealthy-healthy_ab+tlrc'[3]' \
ab224 ranked_unhealthy-healthy_ab+tlrc'[4]' \
ab254 ranked_unhealthy-healthy_ab+tlrc'[5]' \
ab246 ranked
by
kkerr
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AFNI Message Board
For the correlation, I used both R and Excel (same result).
The 3dttest++ output I'm using was a between-groups analysis, but I am using the sub-brick that is specific to one group.
Thank you.
by
kkerr
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AFNI Message Board
I ran a 3dttest++ with two groups and one 1D covariate. The data had been ranked within each group prior to this analysis using 3dTsort. Using 3dmaskdump, I then obtained the values for each subject from the data used in the 3dttest++ analysis for 7 voxels surrounding a peak voxel from the 3dttest++. I then correlated these values with the covariate (within each group) to obtain an estimate of th
by
kkerr
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AFNI Message Board
Thank you. Do you know of any way I could input a group of datasets and have an output of ranked data, so that each subject's dataset would show the rank in comparison to the other subjects? If this were possible, I could then input these datasets into 3dttest++, rank the covariates myself, and run 3dttest++ without the -rankize option to achieve the results I need.
by
kkerr
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AFNI Message Board
I'm not quite clear on what the -rankize option on 3dttest++ does. Here are my questions:
1) How exactly are they ranked? Is it such that, if you had 15 subjects, each voxel in the dataset would be transformed into a rank value (1-15), based on its value in comparison to the other subjects?
2) Is the ranking across groups? For my analysis, I have two groups, and I would prefer for both t
by
kkerr
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AFNI Message Board
We've been using afni_proc.py to process our data and generate @ss_review scripts to review motion and censoring statistics. I recently noticed that for a participant we scanned on Oct. 29 of this year there was a total censor fraction of 2.24, which shouldn't occur since the highest fraction possible should be 1. I looked into the file a little more and discovered that it seems like th
by
kkerr
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AFNI Message Board