Re: [caret-users] read border file into Matlab

2016-11-14 Thread HINDRIKS, RIKKERT
> > Best Regards > Rouhi > > Best Regards > Rouhollah Abdollahi > > *Institut für Neurowissenschaften und Medizin (INM-3)* > Forschungszentrum Jülich > Leo-Brandt-Straße > 52425 Jülich, GermanyTel: +49 2461 61-9324 > > > > On Mon, Nov 14, 2016 at 4:33

Re: [caret-users] read border file into Matlab

2016-11-14 Thread HINDRIKS, RIKKERT
issenschaften und Medizin (INM-3)* > Forschungszentrum Jülich > Leo-Brandt-Straße > 52425 Jülich, GermanyTel: +49 2461 61-9324 > > > > On Mon, Nov 14, 2016 at 11:28 AM, HINDRIKS, RIKKERT < > rikkert.hindr...@upf.edu> wrote: > >> Hi all, >> >> I

[caret-users] read border file into Matlab

2016-11-14 Thread HINDRIKS, RIKKERT
Hi all, Is it possible to load a .border file into Matlab? I am conducting my analysis in Matlab and would like to use the border file of different cortical parcellations for visualization. And generally, what kind of structure does a border file have? Thanks and kind regards, Rikkert Hindrik

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

2015-01-08 Thread HINDRIKS, RIKKERT
. I noticed that in the Paxinos atlas, V5 is merged with the medial wall. On Thu, Jan 8, 2015 at 3:51 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Jan 7, 2015, at 10:16 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, I now have performed the spherical

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

2015-01-07 Thread HINDRIKS, RIKKERT
understand as well. Could you please clearify this for me and tell me how to get a ROI-number for each vertex? Much appreciated! Kind regards, Rikkert On Wed, Nov 5, 2014 at 3:20 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Nov 5, 2014, at 7:05 AM, HINDRIKS, RIKKERT rikkert.hindr

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

2014-11-05 Thread HINDRIKS, RIKKERT
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

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

2014-11-04 Thread HINDRIKS, RIKKERT
). 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

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

2014-11-04 Thread HINDRIKS, RIKKERT
. 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

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

2014-11-04 Thread HINDRIKS, RIKKERT
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

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

2014-10-30 Thread HINDRIKS, RIKKERT
...@brainvis.wustl.edu wrote: 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

[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

Re: [caret-users] Issue with displaying voxel intensities

2014-06-19 Thread HINDRIKS, RIKKERT
see a normal T1w image. If you see solid white, then please upload the volume here, so we can try to replicate the problem: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Donna On Jun 18, 2014, at 12:32 PM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear all, When I load

Re: [caret-users] Issue with displaying voxel intensities

2014-06-19 Thread HINDRIKS, RIKKERT
, 2014, at 1:12 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, I tried to upload the file but am not sure if it worked though. Please let me know... Kind regards, Rikkert On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi

Re: [caret-users] Issue with displaying voxel intensities

2014-06-19 Thread HINDRIKS, RIKKERT
be noted that ~50% of your voxels are NaN, which are generally quite unfriendly to computation such as smoothing. Tim On Thu, Jun 19, 2014 at 2:41 PM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Hi Donna, I'm sorry but I am unable to upload the file... Kind regards, Rikkert

[caret-users] Issue with displaying voxel intensities

2014-06-18 Thread HINDRIKS, RIKKERT
Dear all, When I load a T1-weighted scan into Caret, the image looks like a mask, that is, all white voxels covering the brain. The voxel intensities themselves are, however, nicely distributed and the grey and white matter peaks are clearly visible. Also, the intensities are normalized between 0