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
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Costanza Gianni'
<costanza.gia...@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
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> ha scritto:
Hi Costanza - can you please attach your configuration file?
Best,
a.y
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Costanza Gianni'
<costanza.gia...@uniroma1.it<mailto:costanza.gia...@uniroma1.it>>
Sent: Wednesday, June 5, 2019 6:49:02 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
