[Freesurfer] Freesurfer tutorial datasets v5.1/5.3
External Email - Use Caution Hello FreeSurfer Experts, I'm following the longitudinal FreeSurfer tutorial using v5.1 to become acquainted with stream prior to analyzing our own data. I was able to follow the QDEC tutorial using this version on the Buckner data, however, I kept getting error messages in the QDEC when using the longitudinal data. I created the cross-sectional .dat file using: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat The longitudinal measures (i.e. long.thickness-avg) did not appear in the QDEC, and I've tried to look at thickness alone, and got an error message after hitting 'Analyze'. I assumed these issues were arising due to the fact I downloaded the tutorial dataset for v6, when FreeSurfer v5.1 was installed. I then tried to download the datasets for versions 5.1/5.3, but the files seem to be missing. Can these links be updated? (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data#FreeSurferTutorialDatasets5.1.2BAC8-5.3) Thank you, Amy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer tutorial
Thanks, I've changed the wiki. Can you be more specific about your mri_segstats question? On 8/24/17 2:09 PM, Esteban, Eva(GE Healthcare) wrote: Hello, That worked! Thank you very much. Also, I am trying to understand the information given by mri_segstats and I can find info on the different arguments for the command but not on how to interpret the output. Any recommendations? Thank you! Eva *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* 22 August 2017 17:33 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* EXT: Re: [Freesurfer] Freesurfer tutorial try it without doing any reshaping. If that works, then I'll edit the wiki On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use –reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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 ___ 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] Freesurfer tutorial
Hi, That worked, thank you! From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 22 August 2017 17:33 To: freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Freesurfer tutorial try it without doing any reshaping. If that works, then I'll edit the wiki On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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.
Re: [Freesurfer] Freesurfer tutorial
Hi Eva, Have you taken a look at the help text for mri_segstats (mri_segstats --help)? The information under 'summary file format' and 'examples' may be helpful. Also, this page might have some helpful information for you on working with FreeSurfer stats files: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0 Please let us know if there's anything you'd like us to clarify. Best, Emma From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Esteban, Eva(GE Healthcare) <eva.este...@ge.com> Sent: Thursday, August 24, 2017 2:09 PM To: Freesurfer support list Subject: [Freesurfer] Freesurfer tutorial Hello, That worked! Thank you very much. Also, I am trying to understand the information given by mri_segstats and I can find info on the different arguments for the command but not on how to interpret the output. Any recommendations? Thank you! Eva From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 22 August 2017 17:33 To: freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Freesurfer tutorial try it without doing any reshaping. If that works, then I'll edit the wiki On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use –reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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.
[Freesurfer] Freesurfer tutorial
Hello, That worked! Thank you very much. Also, I am trying to understand the information given by mri_segstats and I can find info on the different arguments for the command but not on how to interpret the output. Any recommendations? Thank you! Eva From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 22 August 2017 17:33 To: freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Freesurfer tutorial try it without doing any reshaping. If that works, then I'll edit the wiki On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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.
Re: [Freesurfer] Freesurfer tutorial
try it without doing any reshaping. If that works, then I'll edit the wiki On 8/22/17 12:00 PM, Esteban, Eva(GE Healthcare) wrote: Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use –reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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.
[Freesurfer] Freesurfer tutorial
Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva ___ 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] freesurfer tutorial data
Instead of FTP, you could try getting the files via HTTP at http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/ -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote: Thx for your responses. But no, I try to copy to my harddrive on my 1 year old Mac. I think for the fith time right now. There should be no limit but I will doublecheck. Best regards. Dix Von meinem iPhone gesendet Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines h...@nmr.mgh.harvard.edu: 2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such. -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: Hi Dix, not sure what's going on. Have you tried multiple times? Bruce On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote: Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de 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] freesurfer tutorial data
2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such. -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: Hi Dix, not sure what's going on. Have you tried multiple times? Bruce On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote: Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de ___ 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] freesurfer tutorial data
Thx for your responses. But no, I try to copy to my harddrive on my 1 year old Mac. I think for the fith time right now. There should be no limit but I will doublecheck. Best regards. Dix Von meinem iPhone gesendet Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines h...@nmr.mgh.harvard.edu: 2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such. -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: Hi Dix, not sure what's going on. Have you tried multiple times? Bruce On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote: Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de 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
[Freesurfer] freesurfer tutorial data
Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de ___ 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] FreeSurfer Tutorial and Workshop
Does anyone know how to register for the FreeSurfer Tutorial and Workshop scheduled for September, 2011? I cannot find a link or a phone number to do this on the Course Description page (http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription). Thanks! Sarah Sarah A. Eisenstein, Ph.D. Postdoctoral Scholar Hershey Lab Psychiatry/Neuroimaging Lab Washington University in St. Louis St. Louis, MO eisenste...@npg.wustl.edu ___ 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] FreeSurfer Tutorial and Workshop
I think you should send an e-mail to Allison (astevens) On Fri, May 27, 2011 at 13:34, Eisenstein, Sarah eisenste...@npg.wustl.eduwrote: Does anyone know how to register for the FreeSurfer Tutorial and Workshop scheduled for September, 2011? I cannot find a link or a phone number to do this on the Course Description page ( http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription). Thanks! Sarah Sarah A. Eisenstein, Ph.D. Postdoctoral Scholar Hershey Lab Psychiatry/Neuroimaging Lab Washington University in St. Louis St. Louis, MO eisenste...@npg.wustl.edu ___ 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] FreeSurfer Tutorial and Workshop
Registration is not open yet and that date is tentative. Once the date is confirmed and registration open, an email will be sent out to the Course mailing list which has a link on the top of the Course Description wiki. Allison On Fri, 27 May 2011, Eisenstein, Sarah wrote: Does anyone know how to register for the FreeSurfer Tutorial and Workshop scheduled for September, 2011? I cannot find a link or a phone number to do this on the Course Description page (http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription). Thanks! Sarah Sarah A. Eisenstein, Ph.D. Postdoctoral Scholar Hershey Lab Psychiatry/Neuroimaging Lab Washington University in St. Louis St. Louis, MO eisenste...@npg.wustl.edu ___ 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] Freesurfer Tutorial and Workshop April 16-18 in Sao Paulo, Brazil
The Freesurfer group and the Hospital das Clinicas from São Paulo University will be offering a three-day Freesurfer Tutorial and Workshop April 16-18 at the Radiology Institute in Sao Paulo, SP, Brazil. A description of the course and a list of the topics covered can be found soon at http://www.neuroimagem.com but it's based on the description of http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The course will take three days this year and will be in English. The registration fee is 400 BRL. If you want to apply for a spot send an e-mail to ppj at netfilter.com.brwith your details. We'll have a form in the website soon. There is room for only 40 participants and registration is on a first-come, first-serve basis. If you are not one of the first 40, you will be put on a waiting list and will be notified if a spot becomes available. If you need any information about arranging payment for the course, accommodations,course location, as well traveling issues please contact me in the e-mail above. Regards, Pedro Paulo Oliveira Jr. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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] FreeSurfer Tutorial and Workshop in Sao Paulo, Brazil
The FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer. Day 1 will be an introduction toFreeSurferhttp://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer (or a refresher for those more experienced). Day 2 will cover everything you need to know for analyzing your data. Topics are listed below. There are only *30 available spots* for this course. The course will not cover FS-FAST neither fMRI analysis. Computers will be provided to all pairs of registrants, which will have FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer and data already installed. Attendees will work in pairs (sharing a computer). The course will be held at Sao Paulo health care complex of HCFMUSP. The lecturers will be: Nick Schmansky, Allison Stevens and Lilla Zollei For more information: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule For requesting a place in the course please write to my e-mail. I think it's a great opportunity for people from Latin America and South Africa. Best Regards, Pedro Paulo Oliveira Jr --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer tutorial
Hello, I am new to using freesurfer. I have installed it successfully and am attempting to go through the tutorial. The tutorial seems to be out of date. I am at the Data Conversion step of the tutorial with the tutorial_subjs directory from the gzipped buckner_data tarball. If I try to run recon-all -i 014-anon/001.dcm -i 015-anon/001.dcm -s anon it complains about the -i flag. It also complained about the -autorecon-all and -autrecon1 flags. Looking through the usage output, I'm guessing that these have been replaced by -all and -stage1 respectively. What has the -i flag been changed too. Forgive my ignorance, if anybody has a changelog or can point me to one, I'd be happy to dig around for this info. Thanks, Gabe Castillo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer tutorial
Hi Gabe, What version of freesurfer are you using? The -autorecon-all, -autorecon1, and -i flags should work with a current version - but are relatively new. If you are using an older version these flags will not work. Could you also send the specific command line and error message you are receiving. When reporting bugs it's really helpful if you included some pertinent information so we can better help you: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks, Jenni On Mon, 27 Feb 2006, Gabe Castillo wrote: Hello, I am new to using freesurfer. I have installed it successfully and am attempting to go through the tutorial. The tutorial seems to be out of date. I am at the Data Conversion step of the tutorial with the tutorial_subjs directory from the gzipped buckner_data tarball. If I try to run recon-all -i 014-anon/001.dcm -i 015-anon/001.dcm -s anon it complains about the -i flag. It also complained about the -autorecon-all and -autrecon1 flags. Looking through the usage output, I'm guessing that these have been replaced by -all and -stage1 respectively. What has the -i flag been changed too. Forgive my ignorance, if anybody has a changelog or can point me to one, I'd be happy to dig around for this info. Thanks, Gabe Castillo ___ 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
[Freesurfer] freesurfer tutorial
Would you consider providing a .pdf version of the web document FreeSurfer Tutorial: Morphometry and Reconstruction that could be easily downloaded and printed out? We occasionally teach a FS class here at the NIH and I know it helps to have a paper-version of the manual to refer to (which is very nice by the way, well-written). Thanks! Peggy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
