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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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Thanks, Rick. It worked. Now, I will double check my PATH. Thanks!!!
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sophia
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AFNI Message Board
Hello, I installed AFNI by following the steps, and to evaluate my whole setup, I typed "afni_system_check.py -check_all". However, it did not work and I've got a message, saying "the command is not found". I wonder where I made errors. Any suggestions will be appreciated.
by
sophia
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AFNI Message Board
Dear Rick,
Oh, thank you very much. Very useful pieces of information that I did not know clearly. I will go through the provided document (afni03_interactive.pdf) to understand them. Many thanks!
Sophia
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sophia
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AFNI Message Board
Thanks for your explanation, Gang.
I think that the result I've got from FSL is based on one-tailed t-test. More specifically, my FSL result came from one of the two contrast, "A-B contrast", showing a significant effect in the experimental group only, but no significant result for B-A contrast in either group. I assume that these may have contributed to the discrepancy (i.e.,
by
sophia
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AFNI Message Board
Hi Rick,
From your comment, "That mask aspect is different from the FDR one. Just to be clear, it is only for volume #3 (for cond:group F), or all of them?", I wonder if the output images (+tlrc) could be multiple... I've got only one output image "DBD_adult_28+tlrc", which looks like the mask.
I viewed the output using AFNI viewer (Underlay = MNI_avg152T1; Overl
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sophia
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AFNI Message Board
Thanks, Gang.
I was specifically requested to show "group x condition/scan" interaction, and for it, I thought 3dLME is the option. As you suggested that this can be done by 3dMVM, too, I will take a look at this program.
In FSL, I ran repeated measure for each group, which is simple group paired t-test, as follows:
The first explanatory variable (EV) was for the condition/sc
by
sophia
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AFNI Message Board
One more question.
As Rick said, it is unlikely to have any significant result from the dataset using 3dLME (two-way repeated ANOVA; 2 groups and 2 conditions/scans with pre- and post-training scans). Before running 3dLEM, I ran a group analysis (i.e., repeated measure) for each group, using FSL (GRF corrected for multiple comparisons, cluster-level thresholding Z > 2.3, p < 0.05). In
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sophia
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AFNI Message Board
Thanks, Rick.
So, when there is no significant result (as indicated by log messages), the output image from that dataset would be typically the group mask (or standard MNI mask: I run 3dLME without using the group mask), which says "no significant result". Is this correct?
Thanks again, Sophia
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sophia
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AFNI Message Board
Thank you for your quick reply, Peter.
Here is the full command and output: (I tried to examine condition*group interaction: 2 groups with ag and ctr; 2 conditions, repeated, with r1 and r2), and input files are resting-state fMRI dataset. I was puzzled when I saw the output file/image, which looks (is) the group mask. Thank you! Sophia
sh -x 3dLME.txt
+ 3dLME -prefix DBD_adult_28 -model
by
sophia
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AFNI Message Board
Hello,
I ran 3dLME and I got the following log message, as well as the outcome image that looks exactly the same as the group mask that I used.
*+ WARNING: Smallest FDR q [3 cond:group F] = 0.466427 ==> few true single voxel detections
Does it simply mean that there was no significant result (e.g. interaction effect)? I thought that the output image/map represents F-score for each
by
sophia
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AFNI Message Board
Hi Gang, the input files were under the current directory where I ran the 3dLME script/text. So, just in case, I removed '' from each line in the script/text (-dataTable), and ran the script/text again. It is now working (giving some logs, such as "Z slice * done: 05/26/17 17:03:23.924 ").
Subj cond group InputFile \
DBD_A00 r1 ag DBD_A00_r1+tlrc '' \
I tho
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sophia
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AFNI Message Board
Hi Gang , thanks for your quick email.
afni -ver
Precompiled binary macosx_10.7_local: May 21 2017 (Version AFNI_17.1.06): this is the AFNI version I used.
The same error was given when I ran it on the lab's server using Version AFNI_16.2.16.
Below is the output on the terminal when I ran 3dLME.txt. I wonder if I made some errors in the setting. Any idea? Many thanks in advance.
S
by
sophia
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AFNI Message Board
I ran 3dLME (2 repeated scans; 2 groups), but input files could not be uploaded, with the following error:
"At least one of the input files has different dimensions!"
Then, I ran 3dinfo -header_line -prefix -same_grid -n4 *.HEAD, which yielded the output as follows:
prefix =grid? Ni Nj Nk Nv
DBD_A00_r1 1 91 109 91 1
DBD_A00_r2 1 91 109 91 1
by
sophia
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AFNI Message Board
Hi Rick,
As suggested some time ago, I used 3dresample with -master option, but yet I got an error message (Input and mask datasets are not same dimensions!). When I checked the resampled mask, # of voxels in each direction was 61 73 61, while the input image had 74 74 40 (both images had the same voxel size, 3mm). What else could I do to force the grids to match?
Thanks,
Sophia
by
sophia
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AFNI Message Board