Hi Nick, can you look into this? I think we fixed this bug in 5.0 or is it something different? Is it still not fixed in 5.1?
Thanks, Martin On Wed, 2011-08-10 at 11:19 -0700, Irwin, William wrote: > Hi- > > Note, this bug still exists in 5.1. Below is my exchange with Martin and Nick > a several months ago. > > -Wil > > --- > |-----Original Message----- > |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] > |Sent: Wednesday, May 25, 2011 3:52 PM > |To: Irwin, William; Martin Reuter > |Subject: RE: 5.1.0 Longitudial syntax question > | > |Martin, > | > |attached is his log. it seems like it will fail if the basename > |partially matches a timepoint name. > | > | > | > |Wil, there are two possible workarounds: > | > |1) edit line 5421 of recon-all to change: > |if ( ! $status) then > | > |to > | > |if ( 0 ) then > | > | > |so that this block is never run > | > |or > | > |2) change the name of the basename so that its not a sub-match, for > |instance change to xxxxxxx_base > | > | > |we'll have to figure out how this happened. > | > |n. > --- > |-----Original Message----- > |From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] > |Sent: Wednesday, August 10, 2011 10:10 AM > |To: Jeff Sadino > |Cc: freesurfer@nmr.mgh.harvard.edu > |Subject: Re: [Freesurfer] Longitudinal Subject/Base name errors > | > |Hi Jeff, > | > |this was a known bug in 5.0 and there are fixes on the web (release notes), > |just download the recon all from there (and did you grab the robust template > |binary)?. > | > |http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > | > |Best, Martin > | > |On Mon, 2011-08-08 at 17:43 -1000, Jeff Sadino wrote: > |> Hello Experts, > |> > |> > |> I am using fs 5.0.0. My naming convention is similar to 100001_S01 > |> and 100001_S02 for subject, and then 100001 for the base. Now when I > |> process the runs longitudinally, I get: ERROR: longitudinal base ID > |> cannot be the same as a timepoint. I believe this is because of line > |> 4845 in recon-all: grep $longbaseid > |> ${longbasedir}/${BaseSubjsListFname} >& /dev/null. I can just as > |> easily cut out this part of the code, or I could manipulate the > |> base-tps file, or rename the base folder. But I do not know if there > |> are other spots in the code that rely on the original naming > |> conventions. Can anyone recommend one approach over the other? > |> > |> > |> Thank you very much, > |> Jeff Sadino > |> _______________________________________________ > |> 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.
