External Email - Use Caution
Thank you Anastasia, I'll try and let you know.
Costanza
Il mer 5 giu 2019, 18:36 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu ha scritto:
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-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 CautionHi 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 CautionHello, 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?
- FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
- Ubuntu 14.04.5 LTS
- 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-cinq...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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-cinq...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer