Re: [Freesurfer] error in longitudinal stream command
External Email - Use Caution Hello Martin, thanks a lot for your reply. It works now, and it was probably an error in my script, though the commands that were used are correct (as per log files), so I still don't know what went wrong. Maybe, for the future, the 'unmatched' error message ought to be adjusted to outline more possible errors. Thanks ! Best, Alex Le mar. 10 sept. 2019, à 03 h 02, Martin Reuter a écrit : > Hi Alexandru, > > not sure what you mean with "unmatched" error. > > If this is still a problem, can you send details? > > Best, Martin > > On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote: > > External Email - Use Caution > > Hello Martin, > > > > I was wondering - how solved the "Unmatched" error ? > > > > In our case, this error appears for both 5.3, 6.0 and dev, on 2 > > different clusters. > > > > All folders exist, are filled with data and reecon-all finished > > without error, plus hippocampus and brainstem > > all folders and readable: drwxrwsrwx (chmod 777 -R) > > In the base-tps - all time points are listed correctly. > > Re-running -base - did not solve the issue. > > Name has no underscores '_' > > > > I didn't have this error on the local installation, so, I suspect it > > might be linked to sourcing some libraries/folders, since we had to > > source the mni folder to make it work. > > > > Best, > > Alexandru. > > > > > > ___ > > 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
Re: [Freesurfer] error in longitudinal stream command
Hi Alexandru, not sure what you mean with "unmatched" error. If this is still a problem, can you send details? Best, Martin On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote: > External Email - Use Caution > Hello Martin, > > I was wondering - how solved the "Unmatched" error ? > > In our case, this error appears for both 5.3, 6.0 and dev, on 2 > different clusters. > > All folders exist, are filled with data and reecon-all finished > without error, plus hippocampus and brainstem > all folders and readable: drwxrwsrwx (chmod 777 -R) > In the base-tps - all time points are listed correctly. > Re-running -base - did not solve the issue. > Name has no underscores '_' > > I didn't have this error on the local installation, so, I suspect it > might be linked to sourcing some libraries/folders, since we had to > source the mni folder to make it work. > > Best, > Alexandru. > > > ___ > 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
Re: [Freesurfer] error in longitudinal stream command
External Email - Use Caution Hello Martin, I was wondering - how solved the "Unmatched" error ? In our case, this error appears for both 5.3, 6.0 and dev, on 2 different clusters. All folders exist, are filled with data and reecon-all finished without error, plus hippocampus and brainstem all folders and readable: drwxrwsrwx (chmod 777 -R) In the base-tps - all time points are listed correctly. Re-running -base - did not solve the issue. Name has no underscores '_' I didn't have this error on the local installation, so, I suspect it might be linked to sourcing some libraries/folders, since we had to source the mni folder to make it work. Best, Alexandru. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error in longitudinal stream command
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 +, 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 +, 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.
Re: [Freesurfer] error in longitudinal stream command
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-boun...@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 +, 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 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.
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 +, 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 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] error in longitudinal stream command
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 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.
