Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
Try this one: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj login pub password download As I recall, though it's been a long time, the GUI Caret took either border or borderproj, but the command line caret_command wanted a borderproj. You indicated you know this is a human target, and you're just getting the feel for it. With monkeys, we use more than the core 6 landmarks. Some of the older tutorials have figures showing more of the sulci. There are many other tools for surface-based registration these days (e.g., ones that use sulc patterns to match without the need to draw landmarks). The connectome project uses MSM: http://www.ncbi.nlm.nih.gov/pubmed/24939340 You can still use Caret, but just making sure you know there are alternatives. On Nov 4, 2014, at 5:23 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, To get a feeling for the registration process in Caret, I start with performing a spherical registration of a human surface to the PALS-atlas. I have extracted the surface and generated a border projection file containing the required cuts and landmarks. However, when I want to perform the registration, I get a massage saying that Caret cannot find the target border projection file. I used this file: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 and indeed, it seems that there is no such file (nor coordinate files for the fiducial and inflated surfaces). Are some files missing or do I do something wrong? Thanks and kind regards, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear Donna, Thanks for your fast response, I appreciate it! My situation is as follows: On the one hand, I have a group-averaged T1-weighted image, together with a volumetric atlas (that is, an integer labeling of the voxels) as well as a structural connectivity matrix (obtained via fiber-tracking on the group-averaged diffusion-weighted image). On the other hand, I have a T1-weighted image of an individual monkey. My aim is to obtain a surface atlas (derived from volumetric atlas) for the individual monkey. This is an interesting scenario, and I've not encountered it before. Could I first to a volumetric-registration of the individual image to the group-averaged image and subsequently project the induced labeling of the voxels of the individual image to the individual surface? This seems reasonable and not too hard. The lower variability in macaque folding may make it less problematic than for humans. Or do I have to extract the surface of the group-averaged image, project the volumetric atlas to it, and subsequently perform a spherical registration of the individual surface to the group- averaged surface? People do extract surfaces from group averaged anatomical volumes for some purposes, but I doubt it will be worth it in this case. I hope others will voice their opinions if they feel otherwise. The first approach seems more straightforward, but I don't know if it is correct. Also, a complication with the second approach is that the extracted surface from the group-averaged image looks worse than that extracted from the individual image (it is entirely ok, except for that the primary visual cortex has a large part missing at the medial side). This is to be expected. A more reasonable thing to do if you want an average surface is generate surfaces for the individuals and compute an average from them. You probably don't have those surfaces, so honestly I'd try the first option and vet the resulting mapping using the T1+contour+volumetric-overlay view. Still another option would be to use surface based registration to get your individual monkey in register with the F6 atlas (part 3, http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_Tutorial_Sep22.pdf) or Donald McLaren's population average macaque atlas (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659879). You could do something like this: * volumetrically warp your atlas goodies to match the mean anatomical McLaren image. * surface-based register your individual macaque atlas to the McLaren standard mesh surface. * map your warped atlas goodies to the McLaren population surface. * view your mapped results on your individual's standard mesh surface. But that second step isn't trivial, and your easier route might suffice. So I'd give that a go first. And Donna, could you please tell me how to create a paint file from a nifty-file? (the atlas I have is saved as a nifti-file) In caret5, Attributes: Map Volume to Surface and choose paint. But getting the color lookup is a bit messy. The newer CIFTI format contains a label lookup table, and
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
Hi Donna, Thanks for the link. Yes, I can imagine that it requires quit some effort (and experience) to register a macaque surface using so many landmarks. I would like to parcellate my macaque cortex using a (high-resolution) atlas. So what about if I do the following: I convert the freesurfer files for both my individual caret-surface and for the F99 standard mesh, register them in freesurfer (or Spherical Demons) and then convert the deformation map to Caret-format (if that's possible). Would this be a good way to go? Kind regards, Rikkert On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Try this one: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj login pub password download As I recall, though it's been a long time, the GUI Caret took either border or borderproj, but the command line caret_command wanted a borderproj. You indicated you know this is a human target, and you're just getting the feel for it. With monkeys, we use more than the core 6 landmarks. Some of the older tutorials have figures showing more of the sulci. There are many other tools for surface-based registration these days (e.g., ones that use sulc patterns to match without the need to draw landmarks). The connectome project uses MSM: http://www.ncbi.nlm.nih.gov/pubmed/24939340 You can still use Caret, but just making sure you know there are alternatives. On Nov 4, 2014, at 5:23 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, To get a feeling for the registration process in Caret, I start with performing a spherical registration of a human surface to the PALS-atlas. I have extracted the surface and generated a border projection file containing the required cuts and landmarks. However, when I want to perform the registration, I get a massage saying that Caret cannot find the target border projection file. I used this file: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 and indeed, it seems that there is no such file (nor coordinate files for the fiducial and inflated surfaces). Are some files missing or do I do something wrong? Thanks and kind regards, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear Donna, Thanks for your fast response, I appreciate it! My situation is as follows: On the one hand, I have a group-averaged T1-weighted image, together with a volumetric atlas (that is, an integer labeling of the voxels) as well as a structural connectivity matrix (obtained via fiber-tracking on the group-averaged diffusion-weighted image). On the other hand, I have a T1-weighted image of an individual monkey. My aim is to obtain a surface atlas (derived from volumetric atlas) for the individual monkey. This is an interesting scenario, and I've not encountered it before. Could I first to a volumetric-registration of the individual image to the group-averaged image and subsequently project the induced labeling of the voxels of the individual image to the individual surface? This seems reasonable and not too hard. The lower variability in macaque folding may make it less problematic than for humans. Or do I have to extract the surface of the group-averaged image, project the volumetric atlas to it, and subsequently perform a spherical registration of the individual surface to the group- averaged surface? People do extract surfaces from group averaged anatomical volumes for some purposes, but I doubt it will be worth it in this case. I hope others will voice their opinions if they feel otherwise. The first approach seems more straightforward, but I don't know if it is correct. Also, a complication with the second approach is that the extracted surface from the group-averaged image looks worse than that extracted from the individual image (it is entirely ok, except for that the primary visual cortex has a large part missing at the medial side). This is to be expected. A more reasonable thing to do if you want an average surface is generate surfaces for the individuals and compute an average from them. You probably don't have those surfaces, so honestly I'd try the first option and vet the resulting mapping using the T1+contour+volumetric-overlay view. Still another option would be to use surface based registration to get your individual monkey in register with the F6 atlas (part 3, http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_Tutorial_Sep22.pdf) or Donald McLaren's population average macaque atlas ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659879). You could do something like this: * volumetrically warp your atlas goodies to match the mean anatomical McLaren image.
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
I doubt you'll be able to convert the deformation map to Caret, but it won't be necessary, if Spherical Demons can resample what you need onto the source or target mesh, after it computes the registration. If it's not too hard, give it a shot and let us know how it goes. On Nov 4, 2014, at 12:59 PM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, Thanks for the link. Yes, I can imagine that it requires quit some effort (and experience) to register a macaque surface using so many landmarks. I would like to parcellate my macaque cortex using a (high-resolution) atlas. So what about if I do the following: I convert the freesurfer files for both my individual caret-surface and for the F99 standard mesh, register them in freesurfer (or Spherical Demons) and then convert the deformation map to Caret-format (if that's possible). Would this be a good way to go? Kind regards, Rikkert On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Try this one: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj login pub password download As I recall, though it's been a long time, the GUI Caret took either border or borderproj, but the command line caret_command wanted a borderproj. You indicated you know this is a human target, and you're just getting the feel for it. With monkeys, we use more than the core 6 landmarks. Some of the older tutorials have figures showing more of the sulci. There are many other tools for surface-based registration these days (e.g., ones that use sulc patterns to match without the need to draw landmarks). The connectome project uses MSM: http://www.ncbi.nlm.nih.gov/pubmed/24939340 You can still use Caret, but just making sure you know there are alternatives. On Nov 4, 2014, at 5:23 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, To get a feeling for the registration process in Caret, I start with performing a spherical registration of a human surface to the PALS-atlas. I have extracted the surface and generated a border projection file containing the required cuts and landmarks. However, when I want to perform the registration, I get a massage saying that Caret cannot find the target border projection file. I used this file: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 and indeed, it seems that there is no such file (nor coordinate files for the fiducial and inflated surfaces). Are some files missing or do I do something wrong? Thanks and kind regards, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear Donna, Thanks for your fast response, I appreciate it! My situation is as follows: On the one hand, I have a group-averaged T1-weighted image, together with a volumetric atlas (that is, an integer labeling of the voxels) as well as a structural connectivity matrix (obtained via fiber-tracking on the group-averaged diffusion-weighted image). On the other hand, I have a T1-weighted image of an individual monkey. My aim is to obtain a surface atlas (derived from volumetric atlas) for the individual monkey. This is an interesting scenario, and I've not encountered it before. Could I first to a volumetric-registration of the individual image to the group-averaged image and subsequently project the induced labeling of the voxels of the individual image to the individual surface? This seems reasonable and not too hard. The lower variability in macaque folding may make it less problematic than for humans. Or do I have to extract the surface of the group-averaged image, project the volumetric atlas to it, and subsequently perform a spherical registration of the individual surface to the group- averaged surface? People do extract surfaces from group averaged anatomical volumes for some purposes, but I doubt it will be worth it in this case. I hope others will voice their opinions if they feel otherwise. The first approach seems more straightforward, but I don't know if it is correct. Also, a complication with the second approach is that the extracted surface from the group-averaged image looks worse than that extracted from the individual image (it is entirely ok, except for that the primary visual cortex has a large part missing at the medial side). This is to be expected. A more reasonable thing to do if you want an average surface is generate surfaces for the individuals and compute an average from them. You probably don't have those surfaces, so honestly I'd try the first option and vet the resulting mapping using the T1+contour+volumetric-overlay view. Still
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
I will try to perform the registration in Caret (since I use Windows, I cannot access the required compiler to run Spherical Demons in Matlab). I found the needed files for registering a macaque cortex and will draw the landmarks by hand. Probably I will have to call for your help again during the process... Kind regards, Rikkert On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker do...@brainvis.wustl.edu wrote: I doubt you'll be able to convert the deformation map to Caret, but it won't be necessary, if Spherical Demons can resample what you need onto the source or target mesh, after it computes the registration. If it's not too hard, give it a shot and let us know how it goes. On Nov 4, 2014, at 12:59 PM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, Thanks for the link. Yes, I can imagine that it requires quit some effort (and experience) to register a macaque surface using so many landmarks. I would like to parcellate my macaque cortex using a (high-resolution) atlas. So what about if I do the following: I convert the freesurfer files for both my individual caret-surface and for the F99 standard mesh, register them in freesurfer (or Spherical Demons) and then convert the deformation map to Caret-format (if that's possible). Would this be a good way to go? Kind regards, Rikkert On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Try this one: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj login pub password download As I recall, though it's been a long time, the GUI Caret took either border or borderproj, but the command line caret_command wanted a borderproj. You indicated you know this is a human target, and you're just getting the feel for it. With monkeys, we use more than the core 6 landmarks. Some of the older tutorials have figures showing more of the sulci. There are many other tools for surface-based registration these days (e.g., ones that use sulc patterns to match without the need to draw landmarks). The connectome project uses MSM: http://www.ncbi.nlm.nih.gov/pubmed/24939340 You can still use Caret, but just making sure you know there are alternatives. On Nov 4, 2014, at 5:23 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, To get a feeling for the registration process in Caret, I start with performing a spherical registration of a human surface to the PALS-atlas. I have extracted the surface and generated a border projection file containing the required cuts and landmarks. However, when I want to perform the registration, I get a massage saying that Caret cannot find the target border projection file. I used this file: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 and indeed, it seems that there is no such file (nor coordinate files for the fiducial and inflated surfaces). Are some files missing or do I do something wrong? Thanks and kind regards, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear Donna, Thanks for your fast response, I appreciate it! My situation is as follows: On the one hand, I have a group-averaged T1-weighted image, together with a volumetric atlas (that is, an integer labeling of the voxels) as well as a structural connectivity matrix (obtained via fiber-tracking on the group-averaged diffusion-weighted image). On the other hand, I have a T1-weighted image of an individual monkey. My aim is to obtain a surface atlas (derived from volumetric atlas) for the individual monkey. This is an interesting scenario, and I've not encountered it before. Could I first to a volumetric-registration of the individual image to the group-averaged image and subsequently project the induced labeling of the voxels of the individual image to the individual surface? This seems reasonable and not too hard. The lower variability in macaque folding may make it less problematic than for humans. Or do I have to extract the surface of the group-averaged image, project the volumetric atlas to it, and subsequently perform a spherical registration of the individual surface to the group- averaged surface? People do extract surfaces from group averaged anatomical volumes for some purposes, but I doubt it will be worth it in this case. I hope others will voice their opinions if they feel otherwise. The first approach seems more straightforward, but I don't know if it is correct. Also, a complication with the second approach is that the extracted surface from the group-averaged image looks worse than that extracted from the individual image (it is entirely
