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 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 >> >>> <http://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 >> >>> <mailto: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 >> >> 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 . 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