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

History of AFNI updates  

|
April 13, 2023 05:43PM
When using 3dUndump, can wildcard characters (e.g., *) be used in the path name?

SCRIPT/CODE:
TEST=/Volumes/Indiv_fMRI_TMS/DX/DATA/Analysed_Data/${SUBJ}/MRI/*_BL1/proc/addt_YYYYMMDD_11111
echo ${TEST}
echo "${Broca_Coor}" | 3dUndump -prefix D_111_Wrk_NativeLoc -srad 1 -orient LPI -master ${TEST}/stats.D_111_REML+orig -xyz -


ERROR:
++ 3dUndump: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]

** glob error: No such file or directory

** You may need to 'setenv AFNI_SHELL_GLOB YES'

**

** In particular, if you are trying to access an NFS (network file

** system) mounted drive, you might be running into the situation

** where the NFS 'cookie' length on the remote system does not

** match the cookie length on your local system -- this is the only

** situation in which we have ever seen this error.  In that case,

** you can either set the environment variable as described above,

** or fix the cookie length mismatch by changing the way the NFS

** drive is exported.

**-------------------------------------------------------------------

** The following information from Graham Wideman of UCSD might also

** be helpful if you are reading this 'glob error' message:

**

**  I've changed the NFS export settings on our Mac OS X 10.5 server

**  to include the '-32bitclients' option, and can confirm that

**  this does cause AFNI to be able to see files that it could not

**  see without this option. So this appears to be the more general

**  way to fix the problem.

**

**  For others in the same boat who may stumble on this message:

**  It's not at all obvious how to actually set this option,

**  as OS X 10.5's Server Admin NFS settings panels don't have

**  any way to do it.

**

**  The short story is:

**  You have to edit the /etc/exports file, as per usual in Unix,

**  but decidedly not in line with all other SharePoint related

**  settings in 10.5.  But first, in order to have the edits not

**  conflict with Server Admin management of those settings, you

**  have to uncheck Server Admin's 'NFS Enabled' checkbox for the

**  relevant shares.  Then, when editing the exports file, move

**  the relevant lines outside the 'Server Admin managed' brackets,

**  and add your options.  In general, such options have to go in

**  the middle section of a line; for example, after the path.

**  Example:

**

** /Somedir -32bitclients -maproot=nobody -sec=sys -network 123.1.2.3 -mask 255.255.255.0

** FATAL ERROR: -master: can't open dataset

has context menu
Subject Author Posted

3dUndump and using wildcard characters (*)

franciss April 13, 2023 05:43PM

Re: 3dUndump and using wildcard characters (*)

rick reynolds April 13, 2023 09:36PM

Re: 3dUndump and using wildcard characters (*)

franciss April 17, 2023 02:26PM