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-cinq...

---

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

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 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-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

Do things not work if you leave it as bedpostx_mgh?

________________________________ 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 12, 2019 8:28:28 AM To: Freesurfer support list Subject: Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

External Email - Use Caution

Dear Anastasia,

I moved to Fressurfer v6.0.0 and I prepared the config file for trac -all. Since I'm running it locally I changed bedpostx_mgh to bedpostx in trac -all accordingly to previous answers found in the archives.

This is the error message I got:

INFO: SUBJECTS_DIR is /home/silvia/spazio/PET INFO: Diffusion root is /home/silvia/spazio/PET Actual FREESURFER_HOME /usr/local/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013 WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx -n 2 /home/silvia/spazio/PET/DOD_C01_recon/dmri subjectdir is /bvecs not found

We assume that the issue is related to 'subjectdir' and bedpostx but I could not fix it. Do you have any suggestion?

We are using fsl version: 5.0.9

thanks a lot,

Costanza

Il giorno mer 5 giu 2019 alle ore 18:36 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <costanza.gianni@uniroma1.itmailto: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.edumailto:AYENDIKI@mgh.harvard.edu> ha scritto: Hi Costanza - can you please attach your configuration file?

Best, a.y ________________________________ 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 Costanza Gianni' <costanza.gianni@uniroma1.itmailto:costanza.gianni@uniroma1.it> Sent: Wednesday, June 5, 2019 6:49:02 AM To: freesurfer@nmr.mgh.harvard.edumailto: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-cinq...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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...