[Freesurfer] Advice for FreeSurfer developers
Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime. Cheers, Ed On 17 Nov 2015, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <564a17d4.6090...@nmr.mgh.harvard.edu<mailto:564a17d4.6090...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, <freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To:freesurfer@nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu/> <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5643680e.1030...@nmr.mgh.harvard.edu<mailto:5643680e.1030...@nmr.mgh.harvard.edu> <mailto:5643680e.1030...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___ Freesurfer mailing list ___ 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.
Re: [Freesurfer] Advice for FreeSurfer developers
This is a good point. We should run the check right away. Right now, the subfield module runs at the end, which means that everything else has completed just fine, but we should definitely check at the very beginning and say: "either download the runtime or remove the subfield flag" Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Gronenschild Ed (NP)" <ed.gronensch...@maastrichtuniversity.nl> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, November 17, 2015 7:09:46 PM Subject: [Freesurfer] Advice for FreeSurfer developers Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime. Cheers, Ed On 17 Nov 2015, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Greve < gr...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer@nmr.mgh.harvard.edu Message-ID: < 564a17d4.6090...@nmr.mgh.harvard.edu > Content-Type: text/plain; charset=windows-1252; format=flowed Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: BQ_BEGIN Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, < freesurfer-requ...@nmr.mgh.harvard.edu < mailto:freesurfer-requ...@nmr.mgh.harvard.edu >> wrote: BQ_BEGIN Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve < gr...@nmr.mgh.harvard.edu < mailto:gr...@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To:freesurfer@ nmr.mgh.harvard.edu < mailto:freesurfer@nmr.mgh.harvard.edu > Message-ID: < 5643680e.1030...@nmr.mgh.harvard.edu < mailto:5643680e.1030...@nmr.mgh.harvard.edu >> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: BQ_BEGIN Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___ Freesurfer mailing list BQ_END BQ_END BQ_END ___ 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 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.
Re: [Freesurfer] Advice for FreeSurfer developers
Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: > Hi Doug, > > I used mostly the default options, nothing special: > > recon-all -autorecon1 -clean-tal -expert my_options.txt -hires > > where the file my_options.txt contains some options for nu_correct. > Then I entered > > recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires > > The error occurred with the last recon-all command. > BTW, I really don't know if the -clean-tal option is needed with FS v6. > > Cheers > Ed > > > On 11 Nov 2015, at 18:00, <freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: > >> Message: 9 >> Date: Wed, 11 Nov 2015 11:08:46 -0500 >> From: Douglas Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] Advice for FreeSurfer developers >> To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <5643680e.1030...@nmr.mgh.harvard.edu >> <mailto:5643680e.1030...@nmr.mgh.harvard.edu>> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Hi Ed, generally recon-all does not need matlab. Are you running the >> gyrification analysis? That should be the only thing that needs matlab. >> doug >> >> On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: >>> Dear developers, >>> >>> Is it possible to check the presence of Matlab runtime right at the >>> start of recon-all >>> in FreeSurfer v6 instead of a long way down in the pipeline. After >>> 36 hours for >>> a high-res data processing I got this unexpected error message. >>> Thanks in advance. >>> >>> Cheers >>> Ed >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Advice for FreeSurfer developers
Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___ 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.
Re: [Freesurfer] Advice for FreeSurfer developers
Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: > Dear developers, > > Is it possible to check the presence of Matlab runtime right at the start of > recon-all > in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours > for > a high-res data processing I got this unexpected error message. > Thanks in advance. > > Cheers > Ed > ___ > 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 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.
Re: [Freesurfer] Advice for FreeSurfer developers
Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, <freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5643680e.1030...@nmr.mgh.harvard.edu<mailto:5643680e.1030...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 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.
