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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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PLEASE DISREGARD! I have solved the issue but not sure how to delete my original post.
Thanks
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willi3by
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AFNI Message Board
Hi,
I am performing a fairly routine analysis where I am aligning a T2 FLAIR to an MNI FLAIR template (first reference to subject, cat_matvec to get the inverse, then applying to get subject to reference). Within 3dAllineate, I am using the -cmass option to get a better alignment. After this initial alignment, I am applying the affine used to warp the subject to reference to an ROI to get it
by
willi3by
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AFNI Message Board
Hi,
I am creating a pipeline to register a CT segmentation in template space to CTs of stroke patients to gather volumetric information (total GM and WM volumes). So far, I perform the following preprocessing on the patient CT (windowing, blurring, skullstrip):
3dcalc -a ROUTINE_HEAD_2_Tilt_1.nii'<0..200>' -expr a -prefix CT_noskull.nii -overwrite
3dBlurToFWHM -input CT_n
by
willi3by
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AFNI Message Board
Of course, it just sounded like perhaps you were saying that first level statistics were necessary for the multivariate modeling performed in the program. Sorry for the misunderstanding.
The data I am working with are derived from a neural network framework through which class activation maps were calculated (range 0-0.5 per voxel). Since the scale of this value is variable for each subject (
by
willi3by
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AFNI Message Board
Interesting, thank you for your reply. I currently have a dataset of "activation" maps that were derived from a separate analysis for subjects in two groups (diseased and healthy) and I am interested in looking at the difference in these maps while controlling for covariates. The maps are raw values so it is simply the Z-stat, not the Fisher-transform. It seems after reading your respon
by
willi3by
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AFNI Message Board
Thank you for your reply! I also disagree with the terminology (hence the quotes), just wanted to stay consistent with what was on the FreeSurfer tutorials.
I will definitely center the qVars, I usually do the pre-checks and centering before inclusion in the MVM script but will look into these options within MVM.
Yes, your description is exactly what I had in mind. I was not sure if 3dMVM
by
willi3by
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AFNI Message Board
Hi,
I have a fairly simple question but I want to make sure I am thinking about glt contrast the right way for 3dMVM. Just for example, let’s say we have two groups with two covariates, age and weight. So the initial mvm set up would include ‘-qVars “Age,Weight”’ and ‘-bsVars Group’
I have some examples of Freesurfer contrast vectors that I want to equate to glt contrasts.
To look at gro
by
willi3by
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AFNI Message Board