Hi Valeria, that is a local install (a frozen version of 5.3 or some modified version from 2013).
Can you source the system wide install of 5.3 and test that. source /space/freesurfer/nmr-stable53-env If that fails, try 6.0 source /space/freesurfer/nmr-stable60-env Also make sure all directories exist, are filled with data and are readable. You can also check the base-tps file in the base and see if all time points are listed there correctly. As a last resort, you can try to re-run the base from scratch and then the long again from scratch. If all that fails, it could be a bug in recon-all (maybe it get's confused with all the _ in the name, but that is unlikely. I also remember we had difficulties with really long names in 5.3 but then it should work with 6.0. Best, Martin On Wed, 2018-08-29 at 17:41 +0000, Barletta, Valeria wrote: > Hi Martin, thanks for your reply. > I tried to re-type the command in the shell but I still have the > error. > I don't know what you mean with system install, but we are using the > version 5.3 and this is the path, if it can help: > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer- > stable5_3_0-05152013 > > Thank you! > Valeria > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-bounces@nmr. > mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard. > edu] > Sent: Wednesday, August 29, 2018 12:14 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error in longitudinal stream command > > Hi Valeria, > > what version of FS are you using (also is it a local install or the > system install)? > > Also try to re-type the command in the shell (don't run it from a > script) could be that there are invisible characters , like tab etc > from copy paste that mess things up. > > Best, Martin > > > On Wed, 2018-08-29 at 13:51 +0000, Barletta, Valeria wrote: > > Dear Freesurfers, > > I am trying to re-launch a longitudinal time point after edits by > > using the command: > > > > recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base > > MS069_base -all > > > > But I am obtaining this type of error: > > > > Unmatched ". > > > > I also tried to launch it on Launchpad but I have an error all the > > same and the process immediately aborts. > > Do you know what could be the reason? > > Thank you, > > Valeria > > > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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.
