They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file.
Any help is appreciated. Regards, Pedro Rosa.
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 greve@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.
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file.
Any help is appreciated. Regards, Pedro Rosa.
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 greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file.
Any help is appreciated. Regards, Pedro Rosa.
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 greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file.
Any help is appreciated. Regards, Pedro Rosa.
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 greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote: > Hi experts, > I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. > > > Any help is appreciated. > Regards, > Pedro Rosa. > > > _______________________________________________ > 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 greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble.
Pedro Rosa
On 21 Aug 2013, at 12:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
> Hi Pedro, see the release notes for the issue > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > doug > > On 08/19/2013 10:06 PM, Pedro Rosa wrote: >> Hi experts, >> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >> >> >> Any help is appreciated. >> Regards, >> Pedro Rosa. >> >> >> _______________________________________________ >> 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 > greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 greve@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
right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or snowleopard?
On 08/21/2013 01:05 PM, Pedro Rosa wrote:
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble.
Pedro Rosa
On 21 Aug 2013, at 12:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote: > Hi, > I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. > Thanks, > Pedro Rosa. > > On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: > >> Hi Pedro, see the release notes for the issue >> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >> doug >> >> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>> Hi experts, >>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>> >>> >>> Any help is appreciated. >>> Regards, >>> Pedro Rosa. >>> >>> >>> _______________________________________________ >>> 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 >> greve@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.
Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 greve@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
Both are mountain lion.
Pedro Rosa
On 21 Aug 2013, at 01:11 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or snowleopard?
On 08/21/2013 01:05 PM, Pedro Rosa wrote:
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble.
Pedro Rosa
On 21 Aug 2013, at 12:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
> They should be fine. BTW, you can run > > recon-all -s subject -make all > > and it will only run the parts that need to be run > > doug > > > On 08/20/2013 12:13 PM, Pedro Rosa wrote: >> Hi, >> I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. >> Thanks, >> Pedro Rosa. >> >> On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >> >>> Hi Pedro, see the release notes for the issue >>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>> doug >>> >>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>> Hi experts, >>>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>>> >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Pedro Rosa. >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> greve@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. > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.lion
On 08/21/2013 01:43 PM, Pedro Rosa wrote:
Both are mountain lion.
Pedro Rosa
On 21 Aug 2013, at 01:11 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or snowleopard?
On 08/21/2013 01:05 PM, Pedro Rosa wrote:
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble.
Pedro Rosa
On 21 Aug 2013, at 12:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote: > Hi, > Sorry for that! > I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' > I used recon-all -s subject -make target > Thank you again, > Pedro Rosa > > On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: > >> They should be fine. BTW, you can run >> >> recon-all -s subject -make all >> >> and it will only run the parts that need to be run >> >> doug >> >> >> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>> Hi, >>> I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. >>> Thanks, >>> Pedro Rosa. >>> >>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >>> >>>> Hi Pedro, see the release notes for the issue >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>> doug >>>> >>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>> Hi experts, >>>>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>>>> >>>>> >>>>> Any help is appreciated. >>>>> Regards, >>>>> Pedro Rosa. >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> greve@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. >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@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
Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
Getting 'make' on Mac systems requires installing XCode AND Command Line Tool. You can download these from Apple using the following link:
https://developer.apple.com/downloads
FYI: This will require opening a developer account (free) if you do not already have one.
-Zeke
On 08/21/2013 12:33 PM, Douglas N Greve wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
> Hi Pedro, see the release notes for the issue > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > doug > > On 08/19/2013 10:06 PM, Pedro Rosa wrote: >> Hi experts, >> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >> >> >> Any help is appreciated. >> Regards, >> Pedro Rosa. >> >> >> _______________________________________________ >> 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 > greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards
Pedro Rosa
On 21 Aug 2013, at 04:16 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Getting 'make' on Mac systems requires installing XCode AND Command Line Tool. You can download these from Apple using the following link:
https://developer.apple.com/downloads
FYI: This will require opening a developer account (free) if you do not already have one.
-Zeke
On 08/21/2013 12:33 PM, Douglas N Greve wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote: > Hi, > I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. > Thanks, > Pedro Rosa. > > On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: > >> Hi Pedro, see the release notes for the issue >> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >> doug >> >> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>> Hi experts, >>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>> >>> >>> Any help is appreciated. >>> Regards, >>> Pedro Rosa. >>> >>> >>> _______________________________________________ >>> 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 >> greve@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.
Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Are all the files you need there? If not, what is missing?
On 08/22/2013 07:41 PM, Pedro Rosa wrote:
Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards
Pedro Rosa
On 21 Aug 2013, at 04:16 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Getting 'make' on Mac systems requires installing XCode AND Command Line Tool. You can download these from Apple using the following link:
https://developer.apple.com/downloads
FYI: This will require opening a developer account (free) if you do not already have one.
-Zeke
On 08/21/2013 12:33 PM, Douglas N Greve wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote:
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
> They should be fine. BTW, you can run > > recon-all -s subject -make all > > and it will only run the parts that need to be run > > doug > > > On 08/20/2013 12:13 PM, Pedro Rosa wrote: >> Hi, >> I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. >> Thanks, >> Pedro Rosa. >> >> On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >> >>> Hi Pedro, see the release notes for the issue >>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>> doug >>> >>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>> Hi experts, >>>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>>> >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Pedro Rosa. >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> greve@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. > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For now I only need brainmask.mgz and wmparc.mgz, so Yes. In case I need other files in the future (i.e. mri_segstats) I plan to run all processing again. Thanks a lot! Pedro Rosa
On 23 Aug 2013, at 11:36 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Are all the files you need there? If not, what is missing?
On 08/22/2013 07:41 PM, Pedro Rosa wrote:
Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards
Pedro Rosa
On 21 Aug 2013, at 04:16 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Getting 'make' on Mac systems requires installing XCode AND Command Line Tool. You can download these from Apple using the following link:
https://developer.apple.com/downloads
FYI: This will require opening a developer account (free) if you do not already have one.
-Zeke
On 08/21/2013 12:33 PM, Douglas N Greve wrote:
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction?
to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have? If I get you the right version, then you might not need the make option.
doug
On 08/21/2013 12:06 PM, Pedro Rosa wrote:
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks
Pedro Rosa
On 21 Aug 2013, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug
On 08/20/2013 10:12 PM, Pedro Rosa wrote: > Hi, > Sorry for that! > I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' > I used recon-all -s subject -make target > Thank you again, > Pedro Rosa > > On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: > >> They should be fine. BTW, you can run >> >> recon-all -s subject -make all >> >> and it will only run the parts that need to be run >> >> doug >> >> >> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>> Hi, >>> I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. >>> Thanks, >>> Pedro Rosa. >>> >>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: >>> >>>> Hi Pedro, see the release notes for the issue >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>> doug >>>> >>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>> Hi experts, >>>>> I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. >>>>> >>>>> >>>>> Any help is appreciated. >>>>> Regards, >>>>> Pedro Rosa. >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> greve@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. >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@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
Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 greve@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/
Hi, I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target
Pedro Rosa
On 20 Aug 2013, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
They should be fine. BTW, you can run
recon-all -s subject -make all
and it will only run the parts that need to be run
doug
On 08/20/2013 12:13 PM, Pedro Rosa wrote:
Hi, I am mainly interested in using the wmparc.mgz files. Are they alright in the subjects with this error in autorecon2? It would be better if I could use this processing, as doing it again in 80 subjects would take a lot of time. Autorecon 1 and 3 ended without errors for all subjects. I inspected the wmparc.mgz files as labels using Slicer 4, and they seem fine. Thanks, Pedro Rosa.
On 20 Aug 2013, at 10:28 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
On 08/19/2013 10:06 PM, Pedro Rosa wrote:
Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file.
Any help is appreciated. Regards, Pedro Rosa.
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 greve@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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@nmr.mgh.harvard.edu
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Douglas N Greve -
Pedro Rosa -
Z K