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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr. mgh.harvard.edu] on behalf of Martin Reuter [mreuter@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

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