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 - 7 of 7
Hi,
I am preparing to do connectivity analyses using task-based data that was pre-processed using fmriprep and then smoothed and scaled in afni.
Similar to resting-state analyses, I would like to clean the data using GLMs and then use the corresponding “errts” datasets. I would like to censor, bandpass filter, model nuisance regressors (e.g., motion parameters), and model periods of “non-in
by
bfuchs
-
AFNI Message Board
Thank you! I was able to specify the encoding to ASCII when generating the files with python. That got rid of the bad characters and the matrices generated by 3dDeconvolve look correct now.
This also was the solution to my issues getting 3dMVM to read my separate -dataTable file.
Thanks again
by
bfuchs
-
AFNI Message Board
Hi experts,
I am running 3dDeconvolve on data from a task with 6 conditions. Data was collected with a block design that consisted of 5 runs, with 1 block of each condition per run. Each run is 160s long, so total scanning time is 800s. When taking a look at the design matrix files (X.xmat.1D, X.nocensor.xmat.1D, X.jpg) generated by 3dDeconvolve, I noticed that blocks from run 1 are not being mo
by
bfuchs
-
AFNI Message Board
Hi,
We are assessing test-retest reliability using ICCb from 3dLME. In seems based on Chen et al. Hum Brain Mapp 2018 that we should be able to get F-statistics for the random effects in addition to the ICC. Is there an option that allows you to specify outputting the F-statistics associated with the ICC values in addition to ICC?
3dLME -prefix $map_folder/${output_name}_fixSession -jobs
by
bfuchs
-
AFNI Message Board
Hi Rick,
Thanks for your reply. We are running a post-5/8 version; the issue ended up not being the version but a missing option in our afni_proc.py script.
Bari
by
bfuchs
-
AFNI Message Board
Hi, thanks for your reply and for the example. We originally had the other components but had left out the 'anat_has_skull no' option. Once we added that to the afni_proc.py script we were able to run the generated script without errors. When we added that option, it removed the following lines from the subject proc script which seemed to be causing the error.
# warp anat follower
by
bfuchs
-
AFNI Message Board
Hi,
We used @SSwarper to skull-strip and warp prior to running afni_proc.py. The @SSwarper finished with no errors and EPI was able to be transformed during the volreg step of afni_proc.py, however we get the following error that we think comes from applying the warp to the structural scan. We copied the cat_matvec line where the error occurred from the generated subject proc file. Attached i
by
bfuchs
-
AFNI Message Board