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Hi, I am not really using any scripts, I am just using the terminal to run and edit everything. As for switching versions of free surfer, we are trying to keep the free surfer version consistent for this project since we have run everything through 6.0 so far.

I have never had this unmatched error before- only when trying to run my longitudinal edits through the longitudinal pipeline. I was able to complete the original longitudinal runs with no problems.

Thank you for your reply! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of hanganu.alexandru@gmail.com hanganu.alexandru@gmail.com Sent: Tuesday, June 9, 2020 9:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unmatched error

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Hi,

I also had this error in the past. It would be reasonable to try and log all the steps now, because I didn't manage to find out where that error was coming from. In my case - I made adjustments to my own scripts.

I can take a look at your scripts, because I didn't manage to recreate that error.

also - it would be probable better to switch to at least FS 6.1

Best, Alex

Le mar. 9 juin 2020, à 10 h 26, COLLEEN PLETCHER <ccpletcher@medicine.wisc.edumailto:ccpletcher@medicine.wisc.edu> a écrit :

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Hello,

I am currently attempting to run a brain through the longitudinal stream after performing edits on the longitudinal brain, using the command recon-all -long timepoint1 base -autorecon2-wm -autorecon3. I am getting an error that says Unmatched ". All of the data for both timepoint 1 and the base is there and readable. I am using version 6.0. Any advice on how to fix this problem?

Thank you!

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Thank you for this list- I was able to get it working! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of hanganu.alexandru@gmail.com hanganu.alexandru@gmail.com Sent: Tuesday, June 9, 2020 11:01 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unmatched error

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Hi,

In this case, there's a list of steps, written by Martin Reuter in one of the previous answers:

check that folders exist, are filled with data and reecon-all finished without error

check that all folders and readable: (chmod 777 -R)

check in the base-tps that all time points are listed correctly

check that names have no underscores '_'

try re-running -base

also: check the names of subjects in the command (recon-all -long ...)

A.

Le mar. 9 juin 2020, à 11 h 04, COLLEEN PLETCHER <ccpletcher@medicine.wisc.edumailto:ccpletcher@medicine.wisc.edu> a écrit :

External Email - Use Caution

Hi, I am not really using any scripts, I am just using the terminal to run and edit everything. As for switching versions of free surfer, we are trying to keep the free surfer version consistent for this project since we have run everything through 6.0 so far.

I have never had this unmatched error before- only when trying to run my longitudinal edits through the longitudinal pipeline. I was able to complete the original longitudinal runs with no problems.

Thank you for your reply! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of hanganu.alexandru@gmail.commailto:hanganu.alexandru@gmail.com <hanganu.alexandru@gmail.commailto:hanganu.alexandru@gmail.com> Sent: Tuesday, June 9, 2020 9:55 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unmatched error

External Email - Use Caution

Hi,

I also had this error in the past. It would be reasonable to try and log all the steps now, because I didn't manage to find out where that error was coming from. In my case - I made adjustments to my own scripts.

I can take a look at your scripts, because I didn't manage to recreate that error.

also - it would be probable better to switch to at least FS 6.1

Best, Alex

Le mar. 9 juin 2020, à 10 h 26, COLLEEN PLETCHER <ccpletcher@medicine.wisc.edumailto:ccpletcher@medicine.wisc.edu> a écrit :

External Email - Use Caution

Hello,

I am currently attempting to run a brain through the longitudinal stream after performing edits on the longitudinal brain, using the command recon-all -long timepoint1 base -autorecon2-wm -autorecon3. I am getting an error that says Unmatched ". All of the data for both timepoint 1 and the base is there and readable. I am using version 6.0. Any advice on how to fix this problem?

Thank you!

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [https://mailfoogae.appspot.com/t?sender=aaGFuZ2FudS5hbGV4YW5kcnVAZ21haWwuY29...