Hi Costanza - When you use "\" in a shell script to continue a command onto the next line, make sure that the "\" is the very last character of the line (see second to last entry in your bvec list.

On a separate note, you'll have to specify the bval file(s).

Best,

a.y

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <costanza.gianni@uniroma1.it>
Sent: Wednesday, June 5, 2019 9:27:12 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

 

        External Email - Use Caution        

Hi Anastasia,

I've attached the configuration file.

Best,

Costanza

Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> ha scritto:

Hi Costanza - can you please attach your configuration file?

Best,
a.y

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <costanza.gianni@uniroma1.it>
Sent: Wednesday, June 5, 2019 6:49:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

 

        External Email - Use Caution        

Hello, FreeSurfer Developers,

I'm trying to run trac -all (I prepared the configuration file following the instructions from v. 5.3) on a set of subjects already processed with recon -all in another computer with a different FREESURFER HOME, and I'm getting this error:

Too many ('s.
INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
INFO: Diffusion root is /home/costanza/extra/PET/PET
Actual FREESURFER_HOME /home/costanza/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
/home/costanza/freesurfer/bin/dmri_motion: Command not found.
/home/costanza/freesurfer/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /home/costanza/freesurfer
    Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
dcmlist: Subscript out of range.

I've searched the list and I couldn't find any similar error. Do you think the main problem is running commands from different FREESURFER HOME?

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

2) Ubuntu 14.04.5 LTS

3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7 14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot for your help,

Costanza

-- 

Costanza Giannì, MD

Radiologist

PhD student

Sapienza University, Rome

+39 348 711 8987

___________________________________________

Il tuo 5 diventa 1000

Fai crescere la tua università

Dona il 5 per mille alla Sapienza

Codice fiscale: 80209930587

https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille

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--

Costanza Giannì, MD

Radiologist

PhD student

Sapienza University, Rome

+39 348 711 8987

___________________________________________

Il tuo 5 diventa 1000

Fai crescere la tua università

Dona il 5 per mille alla Sapienza

Codice fiscale: 80209930587

https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille

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