In the hippocampal subfield segmentation, this happens once every 100-200 subjects. Three for seven is pretty bad. I'll take a look as soon as I can. Cheers, /Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

----- Original Message ----- From: "Claudia Testa" claudia.testa@unibo.it To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, March 31, 2016 11:03:38 AM Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Eugenio,

we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of them. Then we did not carry on with the others. The data are always 3D volumetric FSPGR acquired with the same sequence and scanner. Would you need any other info?

Cheers, Claudia ________________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@bcbl.eu] Inviato: mercoledì 30 marzo 2016 18.56 A: Freesurfer support list Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

----- Original Message ----- From: "Claudia Testa" claudia.testa@unibo.it To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 25, 2016 1:03:42 PM Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376

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

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

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

Hi Eugenio

I have followed your suggestion, specifying -itkthreads 1, although I was already running the process with only one thread. To give you a report: in 12 subjects, 7 brainstem segmentations succeeded, while 5 failed.

The segmentation of one subject failed with the freesurfer version downloaded on the 12 of March, while the segmentation of the same subject worked with the version downloaded on the 20 of March.

The segmentation of 5 subjects failed with both the downloaded versions. We have two types of error as those examples reported in attachment.

Any other suggestions? Thank you

Claudia

________________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@bcbl.eu] Inviato: giovedì 31 marzo 2016 13.08 A: Freesurfer support list Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi again, Claudia. As a temporary workaround, you can use this flag in your recon-all command: -itkthreads 1 This will tell the code not to multithread, which will make it slower, but should help avoid the problems you have experienced. Please let us know how that goes! Cheers, Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

----- Original Message ----- From: "Claudia Testa" claudia.testa@unibo.it To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, March 31, 2016 11:03:38 AM Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Eugenio,

we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of them. Then we did not carry on with the others. The data are always 3D volumetric FSPGR acquired with the same sequence and scanner. Would you need any other info?

Cheers, Claudia ________________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@bcbl.eu] Inviato: mercoledì 30 marzo 2016 18.56 A: Freesurfer support list Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

----- Original Message ----- From: "Claudia Testa" claudia.testa@unibo.it To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 25, 2016 1:03:42 PM Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376

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

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

5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376