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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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Hi Gang,
Many thanks for the reply! It really helps!
I have run 3dAttribute BRICK_STATAUX myFile+tlrc'[##]' and get the following value:
0 4 2 4 88
After referring to this post (https://afni.nimh.nih.gov/afni/community/board/read.php?1,76015,76017#msg-76017), the numerator and denominator should be 4 and 88 respectively right? The first 4 should be the code for statistics, wh
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TracyW
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AFNI Message Board
Hi Rick,
The total length of the out_dir is 46. And the output of "afni -ver" is "Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 'Tiberius')"
BTW, may I know if the output F-statistics in 3dANOVA3 are normalized in the volume? In another way, is it z-transformed?
Since I need to use another function to do the post analysis and it req
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TracyW
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AFNI Message Board
Hi Rick,
Thanks for the reply!
I just fixed the problem. It seems not to be related to the RAM.
In my script, for the output part, I have included the path in the output file name. When I removed those path and only included the file name. It worked.
Maybe 3dANOVA3 cannot tolerant path in the output setting?
The change is as follows:
%%%%%
-adiff 1 2 exper_vs_sham
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TracyW
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AFNI Message Board
Dear AFNI experts,
I have used 3dANOVA3 to run the statistics on my data. However, I have encountered the following crash. The crash log cannot be attached but if you need I can send through email.
I have used 3dANOVA3 before, and it didn't have such crash. Considering if it is out of RAM (Since another script is running taking up 97% memory), I also tested the previous scripts and it s
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TracyW
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AFNI Message Board
Hi Rick,
Yes you are right. The problem is with the missing +orig in the generated script. After adding the missing part, it works fine.
But I didn't alter the proc script before. I don't know what happened since no matter how many times I have tried, the final script is still the same as the missing one. I need to add the missing part manually.
Besides, is it no problem that I u
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TracyW
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AFNI Message Board
Hi Rick,
Thanks for your suggestion.
I have tried the method you suggested. But it seemed didn't work. Since we cannot have the final grid of the processed data until we finish processing, I just used the processed data I did before for other subjects as the master dataset. The used data were following example 11 which used FreeSurfer to segment tissues. And the voxel resolution of the
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TracyW
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AFNI Message Board
Hi Daniel,
Thanks for your reply!
I've tried the dataset you mentioned. But it occured fatal error when processing:
3dmask_tool -input mask_CSFe_resam+tlrc mask_import_Tvent+tlrc -inter -prefix mask_inter_Svent
++ processing 2 input datasets...
++ padding all datasets by 0 (for dilations)
** FATAL ERROR: nvoxel mis-match
It seems the number of voxel of the two masks do not m
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TracyW
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AFNI Message Board
Hi all,
I'm now using AFNI to preprocess resting state fMRI data. As I cannot use FreeSurfer to segment tissues, I plan to use the example 11b to do preprocessing in afni_proc.py.
From the example, it tells us to import a ventricle mask from the template and then using TT space as illustration. And the template used is TT_desai_dd_mpm+tlrc. I'm wondering if there is any template i
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TracyW
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AFNI Message Board
Dear Rick,
Really appreciate to your clear explanation!
Many thanks to your help!
Best regards,
Tracy
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TracyW
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AFNI Message Board
Hi Rick,
Yes, I expected that the BOLD responses vary across the brain. Therefore I used TENT function. And I also think that TENT is more suitable for event-related stimulus right? And my stimulus is event-related not blocked.
For GLT, I have tried without including rest_time.1D following your suggestion. And to make sure I myself do the right analysis, may I write down the steps I did as
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TracyW
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AFNI Message Board
Hi Rick!
Really thanks for your reply!
For your first question, they aren't consecutive short events but single longer (6 s) events. That is to say, each event lasts for 6 seconds(e.g. first 6s showing a "L" on the screen is to ask subjects to do left hand task within the 6s, no matter how many tasks they can perform within the 6s and the same for right hand). And what do you
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TracyW
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AFNI Message Board
Hello? Any one can help?
I have added the '-GOFORIT 2' to the scripts and it seems works fine and ignores the errors and warnings. But is there any side effect if doing so? I'm wondering if those errors occurred because of my regress_stim_times files. Since I have included all stimuli including the baseline time (rest_time.1D).
But if I didn't include it, I can't d
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TracyW
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AFNI Message Board
Hi AFNI experts,
I'm now using proc.py to process fMRI data following the example 6. The scripts are as follows:
**********************************
afni_proc.py -subj_id subj_task12 \
-dsets pre_task?.nii.gz \
-do_block align tlrc \
-copy_a
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TracyW
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AFNI Message Board
Hi Rick,
Thanks for the help. The changed scripts work well actually.
I just found that 3dToutcount can not open the dataset perhaps because of the shared disk I use in my computer. That disk is a shared one for double systems.
When I changed my work directory to the other places, it doesn't throw that error.
BTW, I changed the script a little bit because we found that using the o
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TracyW
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AFNI Message Board
Hi Rick,
Yes, I modified a little bit, the scripts are as follows:
afni_proc.py -subj_id tracy_in1 \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat SUMA/tracy_SurfVol.nii \
-anat_follower_ROI aaseg anat SUMA/aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi SUMA/aparc
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TracyW
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AFNI Message Board
Hi AFNI experts,
I currently preprocessed resting state fMRI data following the example 11a.
However when I used the generated proc. script, it ended soon with the following information:
++ elapsed time = 2.5 s
set tr_counts = ( 200 )
cd tracy_in2.results
touch out.pre_ss_warn.txt
foreach run ( 01 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.tracy_in2.r01.tcat
++ 3d
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TracyW
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AFNI Message Board
Hi AFNI Experts,
I'm now thinking about using AFNI to map two atlas' labels. For example, I have two kinds of atlas, one is AAL 90 atlas which has 90 labels, another is from Freesurfer which has about 160 labels. I'd like to map these two atlas's labels so that I can know the label 1 in AAL90 atlas contains what label numbers in Freesurfer atlas, label 2 in AAL90 atlas con
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TracyW
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AFNI Message Board
Hi Rick,
Thanks for your reply!
For now, I have preprocessed the resting state fMRI data using afni_proc.py. SurfVol works well.
And now I want to use the FreeSurfer-created atlas to get the time series signals and generate correlation matrix in AFNI.
Since I have tried 3dNetCorr directly and get error before. I guess I should do the following steps:
1. create a mask using FreeSurfer
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TracyW
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AFNI Message Board
Hi pt~
I'm also doing the similar analysis as in this post. I just have a question:
how to map the FreeSurfer-created ROIs into the space of the fMRI data?
I tried 3dNetCorr and it tells me that
Data sets of `-inset' and `in_rois' have different numbers of voxels per brik!
I guess the reason is that I didn't map the FreeSurfer-created ROIs into the space of the fMR
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TracyW
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AFNI Message Board
Hi Rick
Thanks for your really clear explanation. I can always learn from your reply!
Yes I have tried your script and it works! The outputs are just as you said. Thank you again!
Tracy
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TracyW
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AFNI Message Board
Hi pt~
Ha ha, yes I blamed windows and just tried the script. It did work! And runs as follows for your reference:
-- will fix any bad char check errors in fixed_preprocess.sh
file 'preprocess.sh': missing final newline
preprocess.sh has 0 bad characters
-- missing final newline was added
** non-Unix check output file 'fixed_preprocess.sh' exists, will overwrite
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TracyW
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AFNI Message Board
Hi pt ~
Thanks for your prompt reply!
I guess it is VirtualBox that makes this problem. Perhaps the linux system can't use the scripts created under windows through VirtualBox. I have tried to create a same file under linux and it succeeded just now.
I'll try Rick's handy tool you mentioned later to see if this can handle. Thank you again!
Best
Tracy
by
TracyW
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AFNI Message Board
Hi AFNI experts!
I'm now using afni_proc.py to generate the script for my resting state preprocessing. I followed example 11 and wrote them into a file named preprocess.sh. I hope to just run this file and get the script.
However, when I run this file using ./preprocess.sh or tcsh preprocess.sh, error occurs., as follows:
** error: unknown trailing arguments : ['\r']
---
by
TracyW
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AFNI Message Board