Hi, if you switch to 5.1 you need to also redo the 20 bases! I would simply rerun everything with 5.1 depending on availability of a cluster. If processing capacities are sparse, just run all bases and long with 5.1 and keep cross sectionals runs in 5.0.
Best, Martin On Aug 11, 2011, at 10:35 PM, Jeff Sadino wrote: > Thank you all for your help. Nick, I installed fs 5.1.0, and it is running > correctly now. This brings up another question though. We have about 200 > subjects (600 scans) we are doing reconstruction on. We are done with the > cross-sectional, and have completed 20 of the base templates, all in fs > 5.0.0. My fs 5.0 installation is running mri_robust_register 1.31.2.1 and > mri_robust_template 1.18.2.3, both dated 7/22/10. Should I update those > binaries with the ones from fs 5.1.0, or would it be better to just do the > rest of the processing (180 templates and 600 long runs) in fs 5.1.0? > > Thank You! > Jeff Sadino > > On Wed, Aug 10, 2011 at 10:27 AM, Nick Schmansky <ni...@nmr.mgh.harvard.edu> > wrote: > stable 5.1 contains the fix, which is the addition of -w to the grep on > line 5428. that particular fix works for the example names given > (100001 as the basename, 100001_S0 and 100001_S1 in the base-tps file). > > can someone give me the basename and base-tps contents so that i can > replicate the problem? > > n. > > On Wed, 2011-08-10 at 14:45 -0400, Martin Reuter wrote: > > 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 > > > | > > > > > > > > > > > > > > > > > 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 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.
