Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 17 of 17
Hi everyone
what would be the correct way to get voxel coordinates from the voxels index in the correlation matrix output by 3dAutoTcorrelate?
thanks!
by
xantossid
-
AFNI Message Board
Hi everyone
I apologize if this question has been already asked : is there an approved processing pipeline you would recommend using to analyze ss-fse imaging?
thanks!
by
xantossid
-
AFNI Message Board
Great all solved! It was indeed an issue with matplotlib I guess the package was broken at some point and I needed to do a fresh install. Now it is all working fine.
Thank you again!
by
xantossid
-
AFNI Message Board
Hi everyone I noticed a problem when running QC (afni_proc option html_review_style pythonic) it is not visualizing qc_02_mot_enormoutlr.jpg and the image is actually an empty file on disk. I am using afni version 19.1.11
Thanks!
by
xantossid
-
AFNI Message Board
Thank you would the fix be already available in release AFNI_19.1.11 ?
by
xantossid
-
AFNI Message Board
Thank you a lot Gang for your help. I have attached the datatable at this link as a text file
Let me know your thoughts
Thanks again
Best regards
by
xantossid
-
AFNI Message Board
Thank you for your reply.
Yes I see the labels in the intercept. I am attaching both files to show this finding. I am using an updated version of afni (downloaded last week).
Does this file represents just the difference in effect magnitude of the levels specified by the variable 'tp' in my case?
Thanks again
by
xantossid
-
AFNI Message Board
Hi Gang
I am running MBA on a control vs patients study and I have a table setup this way:
Subj ROI1 ROI2 Y tp
103 Left_Motor Right_Motor 0.9057 control
..............................
sub1 Left_Motor Right_Motor 0.7641 pat
Now if I run the model with this call
MBA -prefix cont_post -chains 14 -MD -iterations 5000 -model '1+tp' -cVars 'tp&
by
xantossid
-
AFNI Message Board
Hi everyone
I apologize for the silly question but I am confused on how to setup the afni_proc script to analyze my finger tapping fMRI task. The task is basically a subject tapping with all 4 fingers 4 times on the left, then the right hand, then pause 20 seconds, and then repeat another time.
I used the GAM function and I am only able to visualize the left side of the brain results . This was
by
xantossid
-
AFNI Message Board
We are looking for highly motivated candidates to enrich a unique consortium of researchers at The Ohio State University - Center for Neuromodulation. We are looking for a candidate with expertise in MRI, fMRI, PET (optional) image analysis and with a background in programming (Matlab, R, Python). You are expected to take a lead or co-author role in publishing existing data-sets within the lab,
by
xantossid
-
AFNI Message Board
Hi everyone and thank you for maintaining this wonderful community.
I am trying to compare the same 5 subjects scanned on two different 3T scanners with similar resting state fMRI sequence.
Reading the excellent paper of Gang et al. (https://doi.org/10.1002/hbm.23909 ) I decided to use 3dLME with the option -ICCb (below is part of my script) to compare ReHo maps across scanners:
3dLME -pref
by
xantossid
-
AFNI Message Board
Hi everyone
how is TR length impacting ReHo results?
I have performed resting state fmri with TR 2.0 sec and studied reho changes in the cerebellum.
I am now analyzing imaging acquired before this new sequence(same subjects population type): here the voxel size is the same, but we have half of the total number of runs (99 versus 192 of the previous sequence)and the TR is 5.0 . When I process
by
xantossid
-
AFNI Message Board
Thank you Dr Gang for your answer.The thresholding was indeed the problem.
Best regards
by
xantossid
-
AFNI Message Board
HI everyone
I would really appreciate if someone can weight on this: what is the minimum reasonable seed size for resting state fmri (seed to all brain) timeseries extraction. (I'm using HCP ICA cleaned data )
I am trying to correlate tractography findings with resting state fMRI connectivity (seed to all brain) from the thalamus . I have basically parcellated the thalamus using tractogr
by
xantossid
-
AFNI Message Board
Thank you!I will try again with a simpler group of labelmaps as input.
Cheers
by
xantossid
-
AFNI Message Board
Hi everyone
Apologies for the silly question . I am conducting ReHo analysis using 3dReHo. When I use it with the option -in_rois I supply a resampled version of the TTatlas . This dataset has 241 labels as I know from a simple grep on the output of 3dinfo -atlas_points .
But when I process my reho dataset the .vals output file has 237 items.
Another potential issuse I noted is that if I chan
by
xantossid
-
AFNI Message Board