Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2015-01-08 Thread HINDRIKS, RIKKERT
Hi Donna, Thank you very much for your response. You're right about the smoothing: the deformed individual surface in the target directory is indeed the same as the original one (after the flattening). Clear. Would the deformed individual surface in the target directory be considered native

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2015-01-08 Thread Donna Dierker
On Jan 8, 2015, at 11:12 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, Thank you very much for your response. You're right about the smoothing: the deformed individual surface in the target directory is indeed the same as the original one (after the flattening).

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2015-01-07 Thread HINDRIKS, RIKKERT
Hi Donna, I now have performed the spherical registration. What I would need is the PHT atlas on the individual surface. I am however, not sure how to interpret the generated surfaces. For example, in the target directory there appear coordinate files with the prefix deformed and refer to the

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-05 Thread HINDRIKS, RIKKERT
Hi Donna, I've constructed a .borderproj file (and a .bordercolor file) containing the 23 LANDMARKS that correspond to the 23 LANDMARKS in the file Macaque.F99UA1.LR.AVERAGE.LANDMARKS_for_FULL-HEMISPHERE_RegWithPHT00.73730.borderproj with corresponding .bordercolor filee

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-05 Thread Donna Dierker
On Nov 5, 2014, at 7:05 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, I've constructed a .borderproj file (and a .bordercolor file) containing the 23 LANDMARKS that correspond to the 23 LANDMARKS in the file

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread HINDRIKS, RIKKERT
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread Donna Dierker
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread HINDRIKS, RIKKERT
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread Donna Dierker
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread HINDRIKS, RIKKERT
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-31 Thread Donna Dierker
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

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-30 Thread Donna Dierker
On Oct 29, 2014, at 10:56 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear all, I have an averaged T1-image and co-registered volumetric atlas of the macaque brain (which has been digitized by a collaborator) and want to derive from it a surface-based atlas. Subsequently, I

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-30 Thread HINDRIKS, RIKKERT
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

[caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-29 Thread HINDRIKS, RIKKERT
Dear all, I have an averaged T1-image and co-registered volumetric atlas of the macaque brain (which has been digitized by a collaborator) and want to derive from it a surface-based atlas. Subsequently, I would like to use this atlas to get a parcellation of the cortical surface of an individual