Re: [caret-users] SumsDB website can't be reached
Quick! Thanks to Ben & Chip, sumsdb.wustl.edu is up -- at least for the moment. This system is quite dated and would need considerable effort to make it sustainable, so we are in the process of extracting as many archives as possible from it and making them available elsewhere. We are still figuring out how they will be delivered. but for now the process of extracting them from sumsdb is going well. Still, I can't promise that every archive will be extracted, so if you need something, now would be a good time to get it. We hope it will be available for at least another couple of weeks, but keeping it working has been an increasingly uphill battle. I have harvested several F99-related archives here: http://brainmap.wustl.edu/pub/donna/ATLASES/SUMSDB/ROOT/MacaqueZip/ login pub password download Let me know if you need something specific and have trouble finding it. On Jun 29, 2016, at 3:03 PM, Donna Dierker wrote: > I think you will need to follow instructions that more resemble the tutorials > here: > > Caret 5.5 Tutorial - Segmentation, Flattening, and Registration > http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf > > But I'd still read the FS-to-99 document below, because certain sections > (e.g., delineating the medial wall) will still be useful when you follow the > older tutorial. Also, I think the atlas target dataset in the FS-to-F99 > could probably still work with the older Caret 5.5 tutorial. There's a very > good chance David made improvements to the parcellations in the later > dataset, and at the very least, the FS-to-F99 is on the 73730 standard mesh, > which has advantages. > > One gotcha using SureFit-generated segmentations is when you do finally get a > patched hemisphere with no handles that you want to prepare for flattening, > you probably have to convert it to NIFTI and make sure it the correct > voxdims. It's been years since I've done this, but as I recall, we used > monkey T1's with voxdims in the 0.5-0.8mm range, but the volume header didn't > necessarily reflect that. Just make sure when you do the Prepare for > Flattening step, the segmentation volume's header accurately reflects the > voxdims, so that the coordinates in the resulting vtk/coord files are > accurate. > > > On Jun 29, 2016, at 1:12 PM, Cody Sarrazin > wrote: > >> I do not have Freesurfer since I only have access to PCs right now. I am >> also having difficulty finding the tutorials and this is my first experience >> with caret. >> >> Cody >> >> On Tue, Jun 28, 2016 at 1:57 PM, Ting-Yu Chang >> wrote: >> Hi Donna, >> >> Thanks for your reply and help. I segmented our macaque volume data using >> SureFit, not using FreeSurfer. Can I do registration by these datasets? or >> if not, could you or anyone please upload the datasets which can register >> individual SureFit segmentation with F99 atlas? >> >> Thanks very much, >> TingYu >> >> On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker >> wrote: >> It sure would be nice if sumsdb were working right now, but it's not, and I >> have no quick-fix for getting it to work (though we are discussing ideas). >> >> Meanwhile, I'd like to narrow down which F99 individual to F99 registration >> dataset you were looking for. If you segmented your monkey's brain using >> Freesurfer, then maybe archives in this directory might be helpful: >> >> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/ >> login pub >> password download >> >> There was this document: >> >> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc >> (same login/password) >> >> I had these in my download directory, though there is no guarantee they are >> the latest/greatest: >> >> -rw--- 1 donna velab 10272560 Feb 7 2014 FS-to-F99_Aug10.zip >> -rw-r--r-- 1 donna velab 10114922 Apr 3 2014 >> Figs-8-10_architectonic_compare.74k_f99.zip >> -rw-r--r-- 1 donna velab 7797951 Apr 3 2014 >> Figs-3_4_register-F99-with-Chip.R.74k_f99.zip >> -rw-r--r-- 1 donna velab 4729026 Apr 3 2014 >> Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip >> >> I'm cc'ing Chad Donahue, who is a grad student in our lab who does primate >> registration, among other things. >> >> I believe these datasets were the ones cited in this paper: >> >> Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) Cortical >> parcellations of the Macaque monkey analyzed on surface-based atlases. >> Cerebral Cortex doi: 10.1093/cercor/bhr290. >> >> Ting-Gu and Cody: Confirm you have Freesurfer segmentations for your >> monkeys. >> >> Chad: Comment on any later/greater docs/datasets/methods for registering >> monkeys, if they're ready for public use. >> >> Everyone else: Speak up if you have versions of these datasets you >> downloaded from sumsdb. I'm not 100% certain mine are final, but p>.8. >> >> >> On Jun 27, 2016, at 6:58 PM, Cody Sarrazin wrote: >> >>> I actually need these files
Re: [caret-users] SumsDB website can't be reached
I think you will need to follow instructions that more resemble the tutorials here: Caret 5.5 Tutorial - Segmentation, Flattening, and Registration http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf But I'd still read the FS-to-99 document below, because certain sections (e.g., delineating the medial wall) will still be useful when you follow the older tutorial. Also, I think the atlas target dataset in the FS-to-F99 could probably still work with the older Caret 5.5 tutorial. There's a very good chance David made improvements to the parcellations in the later dataset, and at the very least, the FS-to-F99 is on the 73730 standard mesh, which has advantages. One gotcha using SureFit-generated segmentations is when you do finally get a patched hemisphere with no handles that you want to prepare for flattening, you probably have to convert it to NIFTI and make sure it the correct voxdims. It's been years since I've done this, but as I recall, we used monkey T1's with voxdims in the 0.5-0.8mm range, but the volume header didn't necessarily reflect that. Just make sure when you do the Prepare for Flattening step, the segmentation volume's header accurately reflects the voxdims, so that the coordinates in the resulting vtk/coord files are accurate. On Jun 29, 2016, at 1:12 PM, Cody Sarrazin wrote: > I do not have Freesurfer since I only have access to PCs right now. I am also > having difficulty finding the tutorials and this is my first experience with > caret. > > Cody > > On Tue, Jun 28, 2016 at 1:57 PM, Ting-Yu Chang > wrote: > Hi Donna, > > Thanks for your reply and help. I segmented our macaque volume data using > SureFit, not using FreeSurfer. Can I do registration by these datasets? or if > not, could you or anyone please upload the datasets which can register > individual SureFit segmentation with F99 atlas? > > Thanks very much, > TingYu > > On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker > wrote: > It sure would be nice if sumsdb were working right now, but it's not, and I > have no quick-fix for getting it to work (though we are discussing ideas). > > Meanwhile, I'd like to narrow down which F99 individual to F99 registration > dataset you were looking for. If you segmented your monkey's brain using > Freesurfer, then maybe archives in this directory might be helpful: > > http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/ > login pub > password download > > There was this document: > > http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc > (same login/password) > > I had these in my download directory, though there is no guarantee they are > the latest/greatest: > > -rw--- 1 donna velab 10272560 Feb 7 2014 FS-to-F99_Aug10.zip > -rw-r--r-- 1 donna velab 10114922 Apr 3 2014 > Figs-8-10_architectonic_compare.74k_f99.zip > -rw-r--r-- 1 donna velab 7797951 Apr 3 2014 > Figs-3_4_register-F99-with-Chip.R.74k_f99.zip > -rw-r--r-- 1 donna velab 4729026 Apr 3 2014 > Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip > > I'm cc'ing Chad Donahue, who is a grad student in our lab who does primate > registration, among other things. > > I believe these datasets were the ones cited in this paper: > > Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) Cortical > parcellations of the Macaque monkey analyzed on surface-based atlases. > Cerebral Cortex doi: 10.1093/cercor/bhr290. > > Ting-Gu and Cody: Confirm you have Freesurfer segmentations for your monkeys. > > Chad: Comment on any later/greater docs/datasets/methods for registering > monkeys, if they're ready for public use. > > Everyone else: Speak up if you have versions of these datasets you > downloaded from sumsdb. I'm not 100% certain mine are final, but p>.8. > > > On Jun 27, 2016, at 6:58 PM, Cody Sarrazin wrote: > >> I actually need these files as well. >> >> Cody >> >> On Mon, Jun 27, 2016 at 3:33 PM, Ting-Yu Chang >> wrote: >> Hello all, >> >> Recently, the website of SumsDB is unavailable so that we can’t find atlases >> we are looking for. We need data files to register individual scans with the >> standard atlas. Could you help us to fix the problem of website? or could >> you please send me the Macaque F99 atlas datasets for registration with >> individual data? We would also like to request the reference for landmarks. >> >> Thanks, >> >> Ting-Yu >> >> >> >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] SumsDB website can't be reached
I do not have Freesurfer since I only have access to PCs right now. I am also having difficulty finding the tutorials and this is my first experience with caret. Cody On Tue, Jun 28, 2016 at 1:57 PM, Ting-Yu Chang wrote: > Hi Donna, > > Thanks for your reply and help. I segmented our macaque volume data using > SureFit, not using FreeSurfer. Can I do registration by these datasets? or > if not, could you or anyone please upload the datasets which can register > individual SureFit segmentation with F99 atlas? > > Thanks very much, > TingYu > > On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker > wrote: > >> It sure would be nice if sumsdb were working right now, but it's not, and >> I have no quick-fix for getting it to work (though we are discussing ideas). >> >> Meanwhile, I'd like to narrow down which F99 individual to F99 >> registration dataset you were looking for. If you segmented your monkey's >> brain using Freesurfer, then maybe archives in this directory might be >> helpful: >> >> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/ >> login pub >> password download >> >> There was this document: >> >> >> http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc >> (same login/password) >> >> I had these in my download directory, though there is no guarantee they >> are the latest/greatest: >> >> -rw--- 1 donna velab 10272560 Feb 7 2014 FS-to-F99_Aug10.zip >> -rw-r--r-- 1 donna velab 10114922 Apr 3 2014 >> Figs-8-10_architectonic_compare.74k_f99.zip >> -rw-r--r-- 1 donna velab 7797951 Apr 3 2014 >> Figs-3_4_register-F99-with-Chip.R.74k_f99.zip >> -rw-r--r-- 1 donna velab 4729026 Apr 3 2014 >> Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip >> >> I'm cc'ing Chad Donahue, who is a grad student in our lab who does >> primate registration, among other things. >> >> I believe these datasets were the ones cited in this paper: >> >> Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) >> Cortical parcellations of the Macaque monkey analyzed on surface-based >> atlases. Cerebral Cortex doi: 10.1093/cercor/bhr290. >> >> Ting-Gu and Cody: Confirm you have Freesurfer segmentations for your >> monkeys. >> >> Chad: Comment on any later/greater docs/datasets/methods for registering >> monkeys, if they're ready for public use. >> >> Everyone else: Speak up if you have versions of these datasets you >> downloaded from sumsdb. I'm not 100% certain mine are final, but p>.8. >> >> >> On Jun 27, 2016, at 6:58 PM, Cody Sarrazin >> wrote: >> >> > I actually need these files as well. >> > >> > Cody >> > >> > On Mon, Jun 27, 2016 at 3:33 PM, Ting-Yu Chang < >> taiwan.chan...@gmail.com> wrote: >> > Hello all, >> > >> > Recently, the website of SumsDB is unavailable so that we can’t find >> atlases we are looking for. We need data files to register individual scans >> with the standard atlas. Could you help us to fix the problem of website? >> or could you please send me the Macaque F99 atlas datasets for registration >> with individual data? We would also like to request the reference for >> landmarks. >> > >> > Thanks, >> > >> > Ting-Yu >> > >> > >> > >> > >> > >> > ___ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > >> > ___ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > > > -- > -- > Ting-Yu Chang > University of Wisconsin-Madison > Physiology Graduate Training Program > 1-608-335-1628 > tchan...@wisc.edu > 張廷宇 > +886-919-058-196 > taiwan.chan...@gmail.com > > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] SumsDB website can't be reached
Hi Donna, Thanks for your reply and help. I segmented our macaque volume data using SureFit, not using FreeSurfer. Can I do registration by these datasets? or if not, could you or anyone please upload the datasets which can register individual SureFit segmentation with F99 atlas? Thanks very much, TingYu On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker wrote: > It sure would be nice if sumsdb were working right now, but it's not, and > I have no quick-fix for getting it to work (though we are discussing ideas). > > Meanwhile, I'd like to narrow down which F99 individual to F99 > registration dataset you were looking for. If you segmented your monkey's > brain using Freesurfer, then maybe archives in this directory might be > helpful: > > http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/ > login pub > password download > > There was this document: > > > http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc > (same login/password) > > I had these in my download directory, though there is no guarantee they > are the latest/greatest: > > -rw--- 1 donna velab 10272560 Feb 7 2014 FS-to-F99_Aug10.zip > -rw-r--r-- 1 donna velab 10114922 Apr 3 2014 > Figs-8-10_architectonic_compare.74k_f99.zip > -rw-r--r-- 1 donna velab 7797951 Apr 3 2014 > Figs-3_4_register-F99-with-Chip.R.74k_f99.zip > -rw-r--r-- 1 donna velab 4729026 Apr 3 2014 > Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip > > I'm cc'ing Chad Donahue, who is a grad student in our lab who does primate > registration, among other things. > > I believe these datasets were the ones cited in this paper: > > Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) > Cortical parcellations of the Macaque monkey analyzed on surface-based > atlases. Cerebral Cortex doi: 10.1093/cercor/bhr290. > > Ting-Gu and Cody: Confirm you have Freesurfer segmentations for your > monkeys. > > Chad: Comment on any later/greater docs/datasets/methods for registering > monkeys, if they're ready for public use. > > Everyone else: Speak up if you have versions of these datasets you > downloaded from sumsdb. I'm not 100% certain mine are final, but p>.8. > > > On Jun 27, 2016, at 6:58 PM, Cody Sarrazin wrote: > > > I actually need these files as well. > > > > Cody > > > > On Mon, Jun 27, 2016 at 3:33 PM, Ting-Yu Chang > wrote: > > Hello all, > > > > Recently, the website of SumsDB is unavailable so that we can’t find > atlases we are looking for. We need data files to register individual scans > with the standard atlas. Could you help us to fix the problem of website? > or could you please send me the Macaque F99 atlas datasets for registration > with individual data? We would also like to request the reference for > landmarks. > > > > Thanks, > > > > Ting-Yu > > > > > > > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- -- Ting-Yu Chang University of Wisconsin-Madison Physiology Graduate Training Program 1-608-335-1628 tchan...@wisc.edu 張廷宇 +886-919-058-196 taiwan.chan...@gmail.com ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] SumsDB website can't be reached
It sure would be nice if sumsdb were working right now, but it's not, and I have no quick-fix for getting it to work (though we are discussing ideas). Meanwhile, I'd like to narrow down which F99 individual to F99 registration dataset you were looking for. If you segmented your monkey's brain using Freesurfer, then maybe archives in this directory might be helpful: http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/ login pub password download There was this document: http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/FS-to-F99_Tutorial_Sept10.doc (same login/password) I had these in my download directory, though there is no guarantee they are the latest/greatest: -rw--- 1 donna velab 10272560 Feb 7 2014 FS-to-F99_Aug10.zip -rw-r--r-- 1 donna velab 10114922 Apr 3 2014 Figs-8-10_architectonic_compare.74k_f99.zip -rw-r--r-- 1 donna velab 7797951 Apr 3 2014 Figs-3_4_register-F99-with-Chip.R.74k_f99.zip -rw-r--r-- 1 donna velab 4729026 Apr 3 2014 Fig-1A_C_register-F99-with-Chip.R.74k_f99.zip I'm cc'ing Chad Donahue, who is a grad student in our lab who does primate registration, among other things. I believe these datasets were the ones cited in this paper: Van Essen, D.C., Glasser, M.F., Dierker, D. and Harwell, J. (2011) Cortical parcellations of the Macaque monkey analyzed on surface-based atlases. Cerebral Cortex doi: 10.1093/cercor/bhr290. Ting-Gu and Cody: Confirm you have Freesurfer segmentations for your monkeys. Chad: Comment on any later/greater docs/datasets/methods for registering monkeys, if they're ready for public use. Everyone else: Speak up if you have versions of these datasets you downloaded from sumsdb. I'm not 100% certain mine are final, but p>.8. On Jun 27, 2016, at 6:58 PM, Cody Sarrazin wrote: > I actually need these files as well. > > Cody > > On Mon, Jun 27, 2016 at 3:33 PM, Ting-Yu Chang > wrote: > Hello all, > > Recently, the website of SumsDB is unavailable so that we can’t find atlases > we are looking for. We need data files to register individual scans with the > standard atlas. Could you help us to fix the problem of website? or could you > please send me the Macaque F99 atlas datasets for registration with > individual data? We would also like to request the reference for landmarks. > > Thanks, > > Ting-Yu > > > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] SumsDB website can't be reached
Hi Ting-Yu, Hopefully, someone will be able to provide the reference and a link to the dataset for registering individual monkeys to the F99 atlas. If not, I'll dig around tomorrow and try to find it. But I did want to let you know we are aware of the problem with sumsdb. Others have reported it and are waiting for datasets to become available. Unfortunately, there is no quick fix. We are trying to figure out how to get it back up and running as quickly as possible. Donna On Jun 27, 2016, at 4:33 PM, Ting-Yu Chang wrote: > Hello all, > > Recently, the website of SumsDB is unavailable so that we can’t find atlases > we are looking for. We need data files to register individual scans with the > standard atlas. Could you help us to fix the problem of website? or could you > please send me the Macaque F99 atlas datasets for registration with > individual data? We would also like to request the reference for landmarks. > > Thanks, > > Ting-Yu > > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] SumsDB website can't be reached
I actually need these files as well. Cody On Mon, Jun 27, 2016 at 3:33 PM, Ting-Yu Chang wrote: > Hello all, > > Recently, the website of SumsDB is unavailable so that we can’t find > atlases we are looking for. We need data files to register individual > scans with the standard atlas. Could you help us to fix the problem of > website? or could you please send me the Macaque F99 atlas datasets for > registration with individual data? We would also like to request the > reference for landmarks. > > Thanks, > > Ting-Yu > > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] SumsDB website can't be reached
Hello all, Recently, the website of SumsDB is unavailable so that we can’t find atlases we are looking for. We need data files to register individual scans with the standard atlas. Could you help us to fix the problem of website? or could you please send me the Macaque F99 atlas datasets for registration with individual data? We would also like to request the reference for landmarks. Thanks, Ting-Yu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
