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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Colm Connolly
April 18, 2022 11:18AM
Hey,

I'm trying to invoke afni using the -bysub argument to read in a bids dataset of my creation.

I'm running afni as follows 
afni -bysub sub-117 - ./
In this case ./ contains the derivative/sub-XXX/ses-YYY/{anat,func}/sub-xxx_ses-YYY_{T1w,task-rs_bold}.nii.gz files.

Afni complains as follows and only shows the MNI brain with apparently no datasets read in: 
$ afni -bysub sub-117 - ./
** AFNI terminates: I am not a number-- I am a free program!!  [787/895]


Precompiled binary linux_ubuntu_16_64: Apr 14 2022 (Version AFNI_22.1.03 'Antoninus Pius')


** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to S Amara for much encouragement

Initializing: X11[The X.Org Foundation v 12013000].. Widgets...... Input files:[bysub/BIDS]find: warning: you have specified the global option -depth after the argument -type, but global options are not positional, i.e., -depth affects tests specified before it as well as those specified after it.  Please specify global options before other arguments.
find: unknown predicate `-9'

** No datasets found -- making up something **
 Timeseries.1D = 0 files read
 .[tc]sv data  = 0 files read
Path(s) to be searched for plugins: 
/opt/mri_software/linux_ubuntu_16_64 /opt/mri_software/linux_ubuntu_16_64/../lib 

 Plugins       = 50 libraries read
 write compress= GZIP
There appears to be a problem with the construction of the find command invoked by afni.
I'm running afni on: 
Distributor ID:	Ubuntu
Description:	Ubuntu 20.04.4 LTS
Release:	20.04
Codename:	focal
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Subject Author Posted

afni -bysub does not appear to work

Colm Connolly April 18, 2022 11:18AM

Re: afni -bysub does not appear to work

ptaylor April 18, 2022 03:48PM