[Freesurfer] preparing NHP data for whole brain analysis
Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe- sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ 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] preparing NHP data for whole brain analysis
Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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.
Re: [Freesurfer] preparing NHP data for whole brain analysis
Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain
Re: [Freesurfer] preparing NHP data for whole brain analysis
I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Re: [Freesurfer] preparing NHP data for whole brain analysis
Thanks for your input, Donald. Unfortunately, I won't be able to acquire the missing high quality anatomy. Doug, I did not get from the documentation how to use preproc-sess to align data to an NHP atlas in volume space (that is not in human MNI space). Please advise. Thanks! Caspar 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] preparing NHP data for whole brain analysis
If you can get good alignment between the EPI and the T1 images for the 4 subjects with good T1 images, you might try the following: (1) coregister each T1 to the corresponding EPI; (2) normalize the coregistered T1 to the 112RM-SL atlas (see McLaren et al. 2010 in Methods for your options) (3) apply the normalization to EPI data (4) create a mean image from the 4 monkeys (call this the 112RM-SL_EPI and make it public after you publish your paper). (5) use the new EPI atlas to normalize the EPI images. This way all 5 monkeys are aligned to the same template space. If you can create the EPI template in a separate set of animals not in the current experiment, it would be better. You might want to contact Justin Vincent to see if he know any good EPI and T1 datasets in monkeys that could be used to make an EPI template or surfaces for a 112RM-SL surface atlas. Hope this helps. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 6:44 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Thanks for your input, Donald. Unfortunately, I won't be able to acquire the missing high quality anatomy. Doug, I did not get from the documentation how to use preproc-sess to align data to an NHP atlas in volume space (that is not in human MNI space). Please advise. Thanks! Caspar 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial
