AFNI Message Board

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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naiirlab
March 29, 2022 05:08PM
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 ${subjectsDirectory}/${subj}/rest
mkdir motion
3dvolreg -zpad 4 -tshift 0 -base 90 \
-1Dmatrix_save motion/${subj}_vr -nomaxdisp -1Dfile motion/${subj}_vr_motion.1D \
-prefix ${subj}_resting_moco.nii.gz rest.nii.gz


For registration, we are running the following:

echo
echo "Coregistering EPI to anatomical..."
cd ${subjectsDirectory}/${subj}/rest

3dcalc -a ${subj}_resting_moco.nii.gz'[0]' -prefix coreg_slice.nii.gz -expr "a"
flirt -ref ${subjectsDirectory}/${subj}/anat/${subj}_anat_biascorr_brain.nii.gz -in coreg_slice.nii.gz -out coreg_slice_e2a.nii.gz -omat epi2anat.1D -cost corratio -dof 6 -interp trilinear


Any suggestions on why our generated files are shifted?

Please advise.

Thank you!
NAIIRLAB
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Subject Author Posted

Registration Issue - Preprocessing Functional

naiirlab March 29, 2022 05:08PM

Re: Registration Issue - Preprocessing Functional

ptaylor March 29, 2022 09:07PM