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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 2 of 3
Pages: 123
Results 31 - 60 of 67
Hello,
I am having some difficulty figuring out the output of 3dFWHMx on data from +orig space and how to use these data to generate AlphaSim results.
Here are the results from 3dFWHMx for the errts file from a 3dDeconvolve run.
errts_run1+orig (voxel size = 3.9 X 3.9 X 4.8mm): mean x, y, and z values = 4.7
errts_run1+tlrc (voxel size = 2 X 2 X 2 mm): mean x, y, and z values = 5.8
er
by
Christine Smith
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AFNI Message Board
Thank you, James.
I checked out the documentation for 3dblurinmask. It says it is similar to 3dblurtofwhm in that it carries out the operations iteratively. Does that mean that it forces the blur to stop at the specified full width half maximum value? Or does it operate like 3dmerge where it just adds the specified amount of smoothing to the dataset, regardless of the total blurring?
Christ
by
Christine Smith
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AFNI Message Board
Is there something else I can try to figure out why the mask option is not working properly for me?
Regards,
Christine
by
Christine Smith
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AFNI Message Board
Dear Rick,
I just tried it again with even weirder results.
I tried it with the input file masked and using the -mask option. This time it did not blur within the mask at all. The input and output datasets are identical.
Again, when I blur the entire dataset with the mask option all voxels are blurred, inside and outside of the mask.
Just to make sure, the mask is a dataset where i
by
Christine Smith
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AFNI Message Board
Hello,
I am using 3dBlurtoFWHM for the first time and can run it successfully without a mask. I tried to add a mask and it still looks like it is blurring the entire brain. The instructions for the program state that voxels NOT in the mask will be set to zero in the output.
Is there something wrong with this command line?
3dBlurToFWHM -input decon+tlrc -FWHM 4 -mask lhip2mm+tlrc -quiet -p
by
Christine Smith
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AFNI Message Board
Hi Gang,
You are so diplomatic.
Yes, any measure of effect size would be fine.
I know how to calculate cohen's d already (mean difference divided by SD). I realize that I could obtain these values using 3dROIstats on the clusters I found from my ttest sampling the data from each subject.
Maybe it isn't necessary to do this calculation in AFNI afterall?
Christine
by
Christine Smith
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AFNI Message Board
Hello,
Is there an easy way to get eta squared from a t-test?
Or will I need to use 3dcalc? If so, could you help me with how to create the command line?
Regards,
Christine
by
Christine Smith
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AFNI Message Board
Hi Rick,
Thanks for giving my questions so much thought.
I think you are right about clustering just once, after the conjunction.
Best,
Christine
by
Christine Smith
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AFNI Message Board
Hi Gang,
That is funny that you refer me that paper because it is only after reading that paper that I chose to email you in the first place. That paper seems to deal only with the correct way of selecting a p value and describing the appropriate was to test for conjunctions. For the analyses in that paper they used Familywise correction to deal with false positives.
I use cluster-size cor
by
Christine Smith
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AFNI Message Board
Hi Gang,
As far as conjunction analyses are concerned, can you please comment on the two analysis pathways described below that differ in WHEN cluster-extent thresholding is implemented?
It seems to me that method 2 would be overly conservative and would presume that false positives would occur in the same voxel for tests 1 and 2. Is it really necessary to do cluster-extent thresholding af
by
Christine Smith
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AFNI Message Board
Voila!
I took the contents of testtagout.1D and pasted them into a file with the same format as the original .tag file as a final step before asking the Edit Tagset plugin to read it in. The tags are finally in the right spots.
Thank you!
Am I in the running for longest conversation?
by
Christine Smith
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AFNI Message Board
Oops. This is the Vecwarp command I used:
Vecwarp -apar SS01_anat+tlrc -forward -input SS01_tags.tag -output SS01_tags_MNI.tag
by
Christine Smith
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AFNI Message Board
Dear Daniel,
I am exploring the Edit Tagset plugin. This sounds like exactly what I need because I do only want the coordinates of the 6 electrode tips in MNI space.
I made 6 tags in orig space and wrote out the tag locations to SS01_tags.tag
Then I used Vecwarp: Vecwarp -input SS01_anat+tlrc (this is the one transformed to MNI space using @auto_tlrc) -forward -input SS01_tags.tag -out
by
Christine Smith
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AFNI Message Board
UPDATE: When transforming 6 electrode locations, where each location is a point (one voxel) with a different value (1, 2, 3, 4, 5, or 6), the last @auto_tlrc command resulted in only 1 of my points surviving the warp to MNI space. It was in the right spot and had the right value, but the other 5 were lost. Is the NN option working against me because my "regions of interest" are so small
by
Christine Smith
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AFNI Message Board
Hi Daniel,
This is my first time using @auto_tlrc.
For your first option, does this look right?
@auto_tlrc -base MNI_avg152T1+tlrc -input Ax_T1_SPGR_noContrast+orig -dxyz 1
@auto_tlrc -apar Ax_T1_SPGR_noContrast+tlrc -input Electrodes+orig -onewarp -rmode NN
I tried this and the electrode ROIs look like they are in the right place.
Christine
by
Christine Smith
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AFNI Message Board
Hi Rick,
It would be fine to mark the electrodes in orig space and then just transform them to Talairach.
I will carry out this new procedure.
I actually need to get the coordinates of the electrode in MNI space, but I have never used MNI before. I found the following info in a thread on the message board to go from Talairach to MNI.
3dWarp -matvec_out2in mni_fsl2tal.1D -prefix dset
by
Christine Smith
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AFNI Message Board
Hi RIck,
Sorry for the late reply. I thought this message board conversation had moved to an email conversation.
I populated the datasets by looking at a CT showing implanted electrodes fused to a T1 MRI scan using Brainlab software. I took the datasets to AC-PC space in Brainlab.
Then I reconstructed the dicoms in afni for the T1 MRI and took the anatomical dataset to AC-PC space. The
by
Christine Smith
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AFNI Message Board
Hi Rick,
It could be an orientation problem, though I looked at all the datasets and see that they are in RAI. I did "View Images" in to3d and made sure the dicoms were being imported correctly. I may be missing something here...
Next, I transformed the anatomy to AC-PC space and made a copy of it for drawing the ROIs (Dataset Copy: options: fim, datafill->ZeroAll). I drew the
by
Christine Smith
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AFNI Message Board
Hello,
I am experiencing a weird phenomenon with adwarp. I created several ROIs in the frontal lobe and medial temporal lobe in AC-PC space. After manually Talairaching the subject, I adwarped the ROI file to tlrc space.
adwarp -apar Ax_T1_SPGR+tlrc -dpar ROIs+acpc -prefix ROIs
When I load the new ROI+tlrc as an overlay, the ROIs now appear in the cerebellum. :(
I thought of the stup
by
Christine Smith
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AFNI Message Board
and another question...
for the second regressor, it would really only be coding "-1' for condition 1 and "+1" for condition 3. Coding "0" for condition 2 would be indistinguishable from other trials that are coded with zeros, like baseline trials (or any trials that are neither conditions 1, 2, or 3). Isn't this the old problem of effect coding with three co
by
Christine Smith
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AFNI Message Board
Well, Gang, I am probably as excited as you are! I love all the exclamation marks in your previous message.
One more question about how exactly to do this in 3dDevonvolve.
Do I convolve these two regressors with an HRF first? Or can I use minlag and maxlag and then calculate an area under the curve?
Christine
by
Christine Smith
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AFNI Message Board
Dear Gang,
I understand the difficulty of carrying out a linear test in 3dMEMA.
Overall, we are satisfied with the results of 3dRegAna, but our struggle is that we cannot use all of our subjects because they all do not have a sufficient number of trials to generate a reliable beta for each of the three conditions. The result is that the 3dRegAna analysis has a different number of subjects
by
Christine Smith
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AFNI Message Board
Hi Gang,
Thanks for the suggestion. It made me realize that there are a number of scenarios that would "count" as a linear increase across three conditions, that would be missed by doing a conjunction of t-tests. Part of the problem is that with a conjunction analysis, the two components that are combined are thresholded at "nearly" significant (e.g., p = 0.10 for a resulta
by
Christine Smith
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AFNI Message Board
Dear Gang,
We have now carried out the 3dMEMA steps correctly after the suggestion by Isaac (see post below) that the syntax of our code had a problem. We find that with 3dMEMA we obtain 3 clusters, whereas with 3dRegAna on the same subjects we get 18 clusters. The three clusters from 3dMEMA overlap with three of the 18 clusters from 3dRegAna.
I wonder if testing for a linear test using a
by
Christine Smith
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AFNI Message Board
Dear Isaac,
You were right! There was an extra space after one of the "\" symbols. If examined closely it was dark blue, instead of black in our text editor and we missed it. That stopped 3dMEMA at that point in the script. It would explain the error message for the subject following the erroneous space and also the weird degrees of freedom.
Thank you!
Christine
by
Christine Smith
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AFNI Message Board
Dear Gang,
One more piece of information that might be relevant.
We have a question about the t value in 3dMEMA for our paired t-test, which is actually tested as a difference score vs. zero. We noticed that for p = 0.10 the t value was 2.921, and according to a t table, this test would only have 2 degrees of freedom. We have 13 subjects and we think the df should be 12.
Does this soun
by
Christine Smith
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AFNI Message Board
Hi Gang,
Well, the results don't make sense in that there are no findings/clusters using 3dMEMA, whereas there were 18 clusters obtained with a different method (see below). For 3dMEMA, there were a few voxels, mostly outside the brain, and they don't seem to cluster.
I should mention that I am trying to use 3dMEMA to carry out a test of linear increases across three conditions u
by
Christine Smith
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AFNI Message Board
Hello,
I am using 3dMEMA to run a paired t-test, according to Example 3 in the help file.
The program appears to run successfully and it generates the output file. However, it also performs a 3drefit command and then gives me an error message telling me that permission is denied for one of my subjects. Please see the printout below.
The permissions for the offending 'SS06' ar
by
Christine Smith
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AFNI Message Board
Super! Thanks for explaining that. I will come back in off the ledge...
Christine Smith
by
Christine Smith
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AFNI Message Board
Dear Gang,
You wrote: > "I should mention that I turned 3dRegAna into a within-subjects regression by adding 15 vectors, one for each subject. I'm quite impressed by you tricking 3dRegAna into such analysis!"
I should reiterate that it was Doug Ward (as you know, the author of 3dDeconvolve and 3dRegAna) who made this suggestion to me early in the 2000s.
You also wrote
by
Christine Smith
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AFNI Message Board
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Pages: 123