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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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Hi experts,
Is there a function in AFNI to calculate the distance between two MNI coordinates in volumetric space (not surface)? For example, I'd like to calculate the distance between ROI 1 (-68.3,-41.41,-5.14) and ROI 2 (-60.48,-25.22,13.82).
Thanks in advance!
Jenna
by
jblujus
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AFNI Message Board
Thanks Paul and Daniel for your replies! They were very helpful.
Daniel - I just want to make sure I understand. Say you were going to use the master flag in 3dUndump as follows:
3dUndump -prefix ${name}.nii.gz -master sub-001_rest_bold.nii.gz -srad 5 -xyz INFILE
where the sub-001_rest_bold file had an RAI orientation but the coordinates were supplied from LPI orientation.
Considering
by
jblujus
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AFNI Message Board
Hi Paul,
Thanks for the detailed response. For the xyz flag, I fed in one text file per ROI which had 3 columns corresponding to the x,y,z coordinates provided by Power. So, I believe this aligns with your suggestion.
Power's readme file states the following, "All analyses were done in 3mm isotropic voxels in the “KY” atlas at Washington University, using the 4dfp format. The MNI
by
jblujus
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AFNI Message Board
Hi Rick,
Thanks for your response! How would I implement the regression using afni_proc.py?
Thanks,
Jenna
by
jblujus
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AFNI Message Board
Hello,
I am running a resting state analysis. I preprocessed my fMRI and anatomical data using fMRIprep and now I am denoising the data in AFNI. For each model, I am including 24 head motion parameters, volumes identified as non-steady state by fMRIprep, cosine regressors generated by fMRIprep for high-pass filtering, and polort 2 to remove linear trends.
For each subject, I compiled a con
by
jblujus
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AFNI Message Board
Hi all,
I am conducting a resting state fMRI analysis. I preprocessed the data using fMRIprep and denoised the data using AFNI. I would like to create 264 spherical ROIs centered around the MNI coordinates provided by Power et al. (2011; ).
My preprocessed images are in MNI space (MNI152NLin6Asym) with 2x2x2 mm resolution. To create each ROI, I used the following code with 3dUndump:
3dUnd
by
jblujus
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AFNI Message Board
Hi experts,
I am using proc.py to preprocess resting state images, closely following the pipeline laid out in example 11. The options for motion regression include demeaning the 6 motion parameters and entering their derivatives (i.e., 12 total terms). I was wondering if there is a way to expand the motion parameters to 24, for example, in line with Friston's 24 parameter model.
Fristo
by
jblujus
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AFNI Message Board