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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
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Hello! I am looking for assistance with utilizing 3dvolreg for motion correction. After running our 3dvolreg motion correction, we register our EPI to our anatomical utilizing FLIRT within FSL. When we are comparing our motion corrected functional file with the original functional file, we don't notice any differences, which leads us to think there is no motion correct occurring. We have rev
by
naiirlab
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AFNI Message Board
Sorry about that, thank you for trying the command for me.
When I try with '/prefix' I get the following:
++ 3dttest++: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
** FATAL ERROR: 3dttest++: don't recognize option '/prefix' (argv[3])
** Program compile date = Dec 30 2021
Permission denied.
-set
by
naiirlab
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AFNI Message Board
Hello,
I am new to AFNI and am trying to run 3DClustSim, but read how I can run a paired t-test used 3dttest++ invoking -Clustsim
I tried the following: 3dttest++ -Clustsim -AminusB -prefix /{path to group difference file} \
-setA \
{files}
-setB \
but that doesn't seem to work, any suggestions on how to include -Clustsim in my script?
Thank you so much!!
by
naiirlab
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AFNI Message Board
Hi,
We are trying to preprocess our data and have completed the resting state pipeline. There seems to be something wrong during the registration process which we noticed when we tried to QC the results.
We are running the following for motion correction:
echo
echo "Processing functional for ${subj}... "
echo
echo "Motion correction..."
cd ${subjectsDirec
by
naiirlab
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AFNI Message Board
Hi,
This is an FSL script. We have tried messaging the AFNI help too- but no reply back.
Do you know how to bypass the Matlab issue? It's not loading in Matlab so we are trying to convert the file so its not .mat, but nothing has worked yet.
Thank you
by
naiirlab
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AFNI Message Board
Our imaging team is running a pre-processing script on our imaging data, and we are getting the error message ""Could not open matrix file epi2anat.mat"
Here is what our script looks like:
#!/bin/tcsh
# This script does motion correction, field-map correction and registers the functional to the anatomical.
# To QC the results, you need to overlay coreg_slice_e2a over the
by
naiirlab
-
AFNI Message Board