Re: [Freesurfer] Volume to surface
Thank you Anderson,It looks like do just what I want to do, but I'm having a problem, I've give the permissions to make the file an executable as follows chmod +x /root/freesurfer/bin/aseg2surf but when I call it always say that bash: aseg2surf: command not found. My FS v5.1 is working properly and Actually as you can see I'd put the script you sent me into the bin folder on the $FREESURFER_HOME directoryRegards,GabrielEl 07/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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. -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] Volume to surface
Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it.Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time:[root@localhost] srf2obj aseg_004.srf aseg_4.objgawk: /root/freesurfer/bin/srf2obj:2:' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards,GabrielEl 07/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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. -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] Volume to surface
Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink. Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case. All the best! Anderson On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote: Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards, Gabriel El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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] longitudinal study in counterbalance design
Hi, I'd recommend to use time for the order when processing. The order of time points is not relevant in the longitudinal stream but this way the design is more balanced. Best Martin On May 7, 2012, at 23:59, lordowen lordowe...@gmail.com wrote: Hi all: We performed a thickness change study which related to the menstrual cycle. We scanned subjects during different menstrual phases in a counterbalance manner. Thus when we conduct a longitudinal analysis, we need to set time point according to the actual scanning order (i.e., 1st scan as Tp1 and so on) or according to the phase (i.e., menstruation phase as Tp1 and other phase as TpN)? Thanks for your suggestion. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordo...@ms10.hinet.net or lordowe...@gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182 ___ 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] Volume to surface
Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my Linux distribution and is just as you said, the gawk is the default, so I have no any other idea for this.Regards,GabrielEl 08/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink. Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case. All the best! Anderson On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote: Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards, Gabriel El 07/05/12, Anderson Winkler andersonwink...@hotmail.com andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] Volume to surface
Hi Gabriel, Please, try downloading from here: http://dl.dropbox.com/u/2785709/aseg2srf http://dl.dropbox.com/u/2785709/srf2obj Right-click and click Save As, to avoid Windows opening it up and messing up with character encoding. I'll write up a page about the aseg2srf and send the link later... All the best, Anderson On 08/05/12 14:31, Gabriel Gonzalez Escamilla wrote: Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my Linux distribution and is just as you said, the gawk is the default, so I have no any other idea for this. Regards, Gabriel El 08/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió: Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink. Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case. All the best! Anderson On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote: Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards, Gabriel El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@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
[Freesurfer] LongitudinalTutorial and long-tutorial dataset.
Hi, I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example: Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =find . -name 00*.mgz -type l -ls 166617428 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 166617438 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 166783798 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 166783808 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ? Thanks. Natacha Beck ___ 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] Volume to surface
ok, just posted... please, see here: http://brainder.org On 08/05/12 15:51, Anderson Winkler wrote: Hi Gabriel, Please, try downloading from here: http://dl.dropbox.com/u/2785709/aseg2srf http://dl.dropbox.com/u/2785709/srf2obj Right-click and click Save As, to avoid Windows opening it up and messing up with character encoding. I'll write up a page about the aseg2srf and send the link later... All the best, Anderson On 08/05/12 14:31, Gabriel Gonzalez Escamilla wrote: Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my Linux distribution and is just as you said, the gawk is the default, so I have no any other idea for this. Regards, Gabriel El 08/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió: Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink. Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case. All the best! Anderson On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote: Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards, Gabriel El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
Re: [Freesurfer] Volume to surface
Hi Anderson,Now everything works perfectly, thank you so much!!!Best Regards,Gabriel ___ 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] LongitudinalTutorial and long-tutorial dataset.
you can ignore those missing links. the tutorial should still work. n. On Tue, 2012-05-08 at 15:34 +, Natacha Beck, Ms wrote: Hi, I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example: Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =find . -name 00*.mgz -type l -ls 166617428 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 166617438 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 166783798 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 166783808 lrwxrwxrwx1 user1admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz - /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ? Thanks. Natacha Beck ___ 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] RE : LongitudinalTutorial and long-tutorial dataset.
Thank you for your reply, I try to run the first command recon-all -subjid OAS2_0001_MR1 -all and I receive the following trace: Tue May 08 user1 /Applications/freesurfer/subjects/long-tutorial =recon-all -subjid OAS2_0001_MR1 -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110517 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/long-tutorial Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 user1 admin 390840 Jun 24 2011 /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/scripts/recon-all.log Darwin host.ca 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /space/freesurfer/centos4.0_x86_64/stable5 # #@# MotionCor Tue May 8 15:02:39 EDT 2012 Found 2 runs /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/001.mgz /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Seems like FreeSurfer has a problem with the inputs 001.mgz and 002.mgz because it can't reach them. Natacha ___ 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] RE : LongitudinalTutorial and long-tutorial dataset.
you do not need to run recon-all -all on the tutorial subjects, as is stated in the tutorial. its already been processed. On Tue, 2012-05-08 at 19:16 +, Natacha Beck, Ms wrote: Thank you for your reply, I try to run the first command recon-all -subjid OAS2_0001_MR1 -all and I receive the following trace: Tue May 08 user1 /Applications/freesurfer/subjects/long-tutorial =recon-all -subjid OAS2_0001_MR1 -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110517 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/long-tutorial Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 user1 admin 390840 Jun 24 2011 /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/scripts/recon-all.log Darwin host.ca 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /space/freesurfer/centos4.0_x86_64/stable5 # #@# MotionCor Tue May 8 15:02:39 EDT 2012 Found 2 runs /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/001.mgz /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Seems like FreeSurfer has a problem with the inputs 001.mgz and 002.mgz because it can't reach them. Natacha ___ 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.
