Re: [caret-users] Voxel Size for Macaque Anatomicals
John, If you could let me know which works best, .35mm or .5mm isotropic voxels for Macaques, I'd appreciate it. Thank you very much. Best Regards, Donald McLaren = D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (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. - Original Message - From: John Arsenault <[EMAIL PROTECTED]> Date: Thursday, November 2, 2006 10:01 am Subject: [caret-users] Voxel Size for Macaque Anatomicals To: "Caret, SureFit, and SuMS software users" > Hello, > I have an anatomical image taken at .35mm isotropic. For some > reason I > was under the impression that one should resample there data to > .5mm for > registration with the F99 surface. Is this true or is this only for > data of resolution lower the .5mm? As well I was wondering if it was > possible to view the latest segmentation of F99 as well as any > documentation on the smoothing performed after this segmentation? I > know the newest version is suppossed to be more faithful to layer 4 > andI am always interested in having my surfaces represent the > surface as > faithfully as possible. Thank you for your help, > > John___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users >
Re: [caret-users] Voxel Size for Macaque Anatomicals
Donald, I hope Madison is treating you well. Check out part 3 of this tutorial (PDF and zip file in this directory): CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 On 11/03/2006 12:22 PM, DG MCLAREN wrote: David, Awhile ago you mentioned that there were three macaque volumes (F99, F6, Paxinos) and that the F6 was probably best volume target. When I am searching for these, I can only seem to find F99 in SUMSDB. Do you know where the others are located? Also, what is the group surface borders based on? Thank you in advance for your help. Best Regards, Donald McLaren = D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (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. - Original Message - From: David Vanessen <[EMAIL PROTECTED]> Date: Thursday, November 2, 2006 9:30 pm Subject: Re: [caret-users] Voxel Size for Macaque Anatomicals To: "Caret, SureFit, and SuMS software users" John, On Nov 2, 2006, at 9:38 AM, John Arsenault wrote: Hello, I have an anatomical image taken at .35mm isotropic. For some reason I was under the impression that one should resample there data to . 5mm for registration with the F99 surface. Is this true or is this only for data of resolution lower the .5mm? The SureFit algorithm within Caret is designed to work best when the cortex is about 3 voxels thick. This generally translates to 1 mm voxels for human and 0.5 mm voxels for macaque. The algorithm is somewhat flexible, so you might nonetheless get decent segmentation with 0.35 mm voxels. It's an empirical issue, and if your computer is fast it may be worthwhile to try it both ways, then compare segmentation quality. As well I was wondering if it was possible to view the latest segmentation of F99 as well as any documentation on the smoothing performed after this segmentation? I know the newest version is suppossed to be more faithful to layer 4 and I am always interested in having my surfaces represent the surface as faithfully as possible. Thank you for your help, John http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595443&archive_name=Macaque.F99.BOTH-HEMS.STANDARD- SCENES. 73730.spec has the latest version of the F99 surfaces (e.g., Macaque.F99UA1.RIGHT.FIDUCIAL.Std-MESH.73730.coord, Macaque.F99UA1.LEFT.FIDUCIAL.Std-MESH.73730.coord) http://sumsdb.wustl.edu/sums/directory.do? id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6602379&archive_name=Caret_Tutorial_Oct06.pdf has the latest tutorial document, including a tutorial for the F99 macaque atlas. David ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
Re: [caret-users] Voxel Size for Macaque Anatomicals
David, Awhile ago you mentioned that there were three macaque volumes (F99, F6, Paxinos) and that the F6 was probably best volume target. When I am searching for these, I can only seem to find F99 in SUMSDB. Do you know where the others are located? Also, what is the group surface borders based on? Thank you in advance for your help. Best Regards, Donald McLaren = D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (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. - Original Message - From: David Vanessen <[EMAIL PROTECTED]> Date: Thursday, November 2, 2006 9:30 pm Subject: Re: [caret-users] Voxel Size for Macaque Anatomicals To: "Caret, SureFit, and SuMS software users" > John, > > On Nov 2, 2006, at 9:38 AM, John Arsenault wrote: > > > Hello, > > I have an anatomical image taken at .35mm isotropic. For some > > reason I > > was under the impression that one should resample there data to . > > 5mm for > > registration with the F99 surface. Is this true or is this only for > > data of resolution lower the .5mm? > > The SureFit algorithm within Caret is designed to work best when > the > cortex is about 3 voxels thick. This generally translates to 1 mm > voxels for human and 0.5 mm voxels for macaque. > > The algorithm is somewhat flexible, so you might nonetheless get > decent segmentation with 0.35 mm voxels. It's an empirical issue, > and if your computer is fast it may be worthwhile to try it both > ways, then compare segmentation quality. > > > > As well I was wondering if it was > > possible to view the latest segmentation of F99 as well as any > > documentation on the smoothing performed after this segmentation? > I > > know the newest version is suppossed to be more faithful to layer > 4 > > and > > I am always interested in having my surfaces represent the > surface as > > faithfully as possible. Thank you for your help, > > > > > John > > > http://sumsdb.wustl.edu/sums/archivelist.do? > archive_id=6595443&archive_name=Macaque.F99.BOTH-HEMS.STANDARD- > SCENES. > 73730.spec > > has the latest version of the F99 surfaces (e.g., > Macaque.F99UA1.RIGHT.FIDUCIAL.Std-MESH.73730.coord, > Macaque.F99UA1.LEFT.FIDUCIAL.Std-MESH.73730.coord) > > http://sumsdb.wustl.edu/sums/directory.do? > id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > http://sumsdb.wustl.edu/sums/archivelist.do? > archive_id=6602379&archive_name=Caret_Tutorial_Oct06.pdf > > has the latest tutorial document, including a tutorial for the F99 > macaque atlas. > > David > >
Re: [caret-users] Voxel Size for Macaque Anatomicals
John, On Nov 2, 2006, at 9:38 AM, John Arsenault wrote: Hello, I have an anatomical image taken at .35mm isotropic. For some reason I was under the impression that one should resample there data to . 5mm for registration with the F99 surface. Is this true or is this only for data of resolution lower the .5mm? The SureFit algorithm within Caret is designed to work best when the cortex is about 3 voxels thick. This generally translates to 1 mm voxels for human and 0.5 mm voxels for macaque. The algorithm is somewhat flexible, so you might nonetheless get decent segmentation with 0.35 mm voxels. It's an empirical issue, and if your computer is fast it may be worthwhile to try it both ways, then compare segmentation quality. As well I was wondering if it was possible to view the latest segmentation of F99 as well as any documentation on the smoothing performed after this segmentation? I know the newest version is suppossed to be more faithful to layer 4 and I am always interested in having my surfaces represent the surface as faithfully as possible. Thank you for your help, John http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595443&archive_name=Macaque.F99.BOTH-HEMS.STANDARD-SCENES. 73730.spec has the latest version of the F99 surfaces (e.g., Macaque.F99UA1.RIGHT.FIDUCIAL.Std-MESH.73730.coord, Macaque.F99UA1.LEFT.FIDUCIAL.Std-MESH.73730.coord) http://sumsdb.wustl.edu/sums/directory.do? id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6602379&archive_name=Caret_Tutorial_Oct06.pdf has the latest tutorial document, including a tutorial for the F99 macaque atlas. David
[caret-users] Voxel Size for Macaque Anatomicals
Hello, I have an anatomical image taken at .35mm isotropic. For some reason I was under the impression that one should resample there data to .5mm for registration with the F99 surface. Is this true or is this only for data of resolution lower the .5mm? As well I was wondering if it was possible to view the latest segmentation of F99 as well as any documentation on the smoothing performed after this segmentation? I know the newest version is suppossed to be more faithful to layer 4 and I am always interested in having my surfaces represent the surface as faithfully as possible. Thank you for your help, John
