yes, I will test it. i'm kind of new to symbolic links. thanks! Jon
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
Yes, the directories and files will all exist under the Dropbox folder and will thus be backed up by Dropbox. But I suggest you test this for yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer