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 space? The only difference with
the unregistered surface is that it is resampled onto standard mesh (but
the shape is the same). All goodies also
project nicely to it. I also plotted them over one another and they
perfectly overlap. FYI: I am calculating an EcoG
leadfield on the surface so the exact shape needs to stay the same.

And am I correct that the deformed template surfaces in the source
directory are resampled onto the individual
mesh? In this directory, however, I only see the deformed spherical. I that
all the boxes Deform coordinate files to
atlas so these I assume, are the deformed surfaces in the target
directory. I see however, no box atlas to individual.

I figured out how to export a paint file and input it in Matlab: I save it
as a labeled GIFTI file and open it in Matlab
with gifti.m (from the GIFTI toolbox). I then have all 19 columns at once!

Kind regards,
Rikkert

P.S. 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 registration. What I would need is
 the PHT atlas on the individual surface.

 If you checked the box requesting atlas to individual, then you should
 have that in your individual/source directory.

  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 individual
 monkey. Although the shape of the fiducial
  one is very similar to the shape of the (undeformed) individual surface,
 there are some slight differences (for
  example, the medial wall is smoothed). What is the exact interpretation
 of these surfaces?

 Yes, the medial wall gets smoothed at the beginning of flattening, if I
 recall correctly (it's been a long time!), and a version of the sphere is
 generated from the fiducial with the smoothed medial wall.  This is what
 goes into registration.

 What you are seeing in the atlas directory is the source/individual
 midthickness (with smoothed medial wall) resampled onto the target mesh.
 It will be slighter smoother than the source, and thus have slightly
 smaller surface area.  But it will look a lot like the source.

  I noticed that I can view the different atlases defined on the template
 on these deformed atlases. Does this
  mean that I have mapped them to the individual surface (which is what I
 want)?

 It sounds like things went reasonably well.  Now you're at a point where
 you need to decide:

 * do I work with atlas goodies on my native individual surface
 (assuming you checked that box)? or
 * do I work with individual goodies on atlas surfaces

 The answer depends on what you're doing with the data.  If it's more
 important that the surface stays native (e.g., for folding/areal
 measurements), then the former option is better.  If it's handy to have
 things on the atlas standard mesh for other reasons, then atlas-land is the
 way to go.  With just one subject, native-land may be fine.  I did skim the
 history below, but don't have the time to fully digest it at the moment.
 But maybe this will get you further along in your own thinking about next
 steps.

  One more question about exporting the results: When I export the
 deformed surface with the atlas as a
  .label.gii file and read it into Matlab, I get a nice list of ROI names
 and corresponding RGB and alpha
  values. However, the .cdata fields has 20 columns which I don't
 understand. I hoped to get, for each
  vertex, an index into the ROI list. I've also tried to export it as a
 surf.gii file, the then the .cdata field has
  4 columns whose meaning I don't understand as well. Could you please
 clearify this for me and tell me
  how to get a ROI-number for each vertex?

 The atlas label/paint file may have multiple columns for multiple
 parcellations (e.g., LVE00 vs OrbitalFrontal).  You might need to extract
 just one of these and work with a single parcellation at a time.  This is
 my best guess as to what is going on there.

 
  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...@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
 Macaque.F99UA1.LR.AVERAGE.LANDMARKS_for_FULL-HEMISPHERE_RegWithPHT00.73730.borderproj
 with
   corresponding .bordercolor 

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). Clear.
 
 Would the deformed individual surface in the target directory be considered 
 native space? The only difference with
 the unregistered surface is that it is resampled onto standard mesh (but the 
 shape is the same).

The deformed surface is in the same *stereotaxic space* as the source surface.

The surfaces in the atlas directory are on the same mesh as the atlas surface.

 All goodies also
 project nicely to it. I also plotted them over one another and they perfectly 
 overlap. FYI: I am calculating an EcoG
 leadfield on the surface so the exact shape needs to stay the same.

I would think you'd want to work on native mesh, then (individual/source 
directory).

 And am I correct that the deformed template surfaces in the source directory 
 are resampled onto the individual
 mesh? In this directory, however, I only see the deformed spherical. I that 
 all the boxes Deform coordinate files to
 atlas so these I assume, are the deformed surfaces in the target directory. 
 I see however, no box atlas to individual.

Whatever files were in the atlas/target spec file when you ran registration 
will get resampled onto the source subject's mesh and saved in the source 
directory.  You can also apply the deform_map in the source dir to your atlas 
goodies, or just re-run registration using a spec file that points to the 
goodies you want resampled onto native mesh.

 I figured out how to export a paint file and input it in Matlab: I save it as 
 a labeled GIFTI file and open it in Matlab
 with gifti.m (from the GIFTI toolbox). I then have all 19 columns at once!

Now you have to ponder which are useful to you.

 Kind regards,
 Rikkert
 
 P.S. 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 registration. What I would need is the 
  PHT atlas on the individual surface.
 
 If you checked the box requesting atlas to individual, then you should have 
 that in your individual/source directory.
 
  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 individual 
  monkey. Although the shape of the fiducial
  one is very similar to the shape of the (undeformed) individual surface, 
  there are some slight differences (for
  example, the medial wall is smoothed). What is the exact interpretation of 
  these surfaces?
 
 Yes, the medial wall gets smoothed at the beginning of flattening, if I 
 recall correctly (it's been a long time!), and a version of the sphere is 
 generated from the fiducial with the smoothed medial wall.  This is what goes 
 into registration.
 
 What you are seeing in the atlas directory is the source/individual 
 midthickness (with smoothed medial wall) resampled onto the target mesh.  It 
 will be slighter smoother than the source, and thus have slightly smaller 
 surface area.  But it will look a lot like the source.
 
  I noticed that I can view the different atlases defined on the template on 
  these deformed atlases. Does this
  mean that I have mapped them to the individual surface (which is what I 
  want)?
 
 It sounds like things went reasonably well.  Now you're at a point where you 
 need to decide:
 
 * do I work with atlas goodies on my native individual surface 
 (assuming you checked that box)? or
 * do I work with individual goodies on atlas surfaces
 
 The answer depends on what you're doing with the data.  If it's more 
 important that the surface stays native (e.g., for folding/areal 
 measurements), then the former option is better.  If it's handy to have 
 things on the atlas standard mesh for other reasons, then atlas-land is the 
 way to go.  With just one subject, native-land may be fine.  I did skim the 
 history below, but don't have the time to fully digest it at the moment.  But 
 maybe this will get you further along in your own thinking about next steps.
 
  One more question about exporting the results: When I export the deformed 
  surface with the atlas as a
  .label.gii file and read it into Matlab, I get a nice list of ROI names and 
  corresponding RGB and alpha
  values. However, the .cdata fields has 20 columns which I don't understand. 
  I hoped to get, for each
  vertex, an index into the ROI list. I've also tried to export it as a 
  surf.gii file, the then the .cdata field has
  4 columns whose meaning I don't understand as well. Could you please 
  clearify this for me and tell 

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 individual
monkey. Although the shape of the fiducial
one is very similar to the shape of the (undeformed) individual surface,
there are some slight differences (for
example, the medial wall is smoothed). What is the exact interpretation of
these surfaces?

I noticed that I can view the different atlases defined on the template on
these deformed atlases. Does this
mean that I have mapped them to the individual surface (which is what I
want)?

One more question about exporting the results: When I export the deformed
surface with the atlas as a
.label.gii file and read it into Matlab, I get a nice list of ROI names and
corresponding RGB and alpha
values. However, the .cdata fields has 20 columns which I don't understand.
I hoped to get, for each
vertex, an index into the ROI list. I've also tried to export it as a
surf.gii file, the then the .cdata field has
4 columns whose meaning I don't 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...@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
 Macaque.F99UA1.LR.AVERAGE.LANDMARKS_for_FULL-HEMISPHERE_RegWithPHT00.73730.borderproj
 with
  corresponding .bordercolor filee
 Macaque.LANDMARKS_for_FULL-HEM.bordercolor and I think there is a good
 correspondence
  between the individual and template LANDMARKS.
 
  To perform the spherical registration however, I need the template
 sphere of the left hemisphere, while I can only find the one of the
  right hemisphere (Macaque.ATLAS.sphere.6.73730.coord). Do you know where
 I can find it? (Maybe I can obtain it by mirroring, but
  I have no idea how this could be done).

 Use the right for both.  Caret with x-flip the left hems when it does its
 thing, provided the source spec file correctly identifies the hemisphere.

 In this way, the resulting left and right hem resampled surfaces are in
 register with one another.

 Just make sure there is a hemisphere tag that correctly identifies your
 left hem, and Caret will do the rest.

  And I have a couple of general questions:
 
  1. In which file-types are the sulcal-depths stored? (this applies both
 to individual as well as template data)?  I quess this should be a
  .surface_shape file, but I cannot find it. I ask this because I want to
 make a new directory which only contains those files that I need.

 Should be surface_shape, but depending on what spec file you are using,
 you might not have one.  Or if it is more recent, it might be shape.gii.
 The Sept 2006 tutorial has a surface_shape for the macaque F99 in the
 MACAQUE subdir, for example.

 If your individual was segmented in Caret, then it should have a sulcal
 depth map from the prepare for flattening step.  This should be in a
 surface shape file.  If you used something else, then are you sure you need
 the sulcal depth map?  If you just want something that looks like it for
 visualization, the Freesurfer .sulc is a good substitute.

  2. In connection with this: What is the best way to organize the data
 files? I now make different folders (one  for flattening, one for
  landmarks, and one for the registration, each containing a different set
 of data files and a single .spec file). Should I put everything
  in one folder and make different .spec files for the different
 procedures?

 One hem, different specs.

  3. Why are there .topology files? (since the topology is determined by
 the triangulation, which is stored in .coord files)

 Coords contain only x,y,z coordinates.  Neighbor relationships are in the
 .topo files.

  4. After registering, how can I project any goodies defined on the
 template to the individual surface?

 Make sure the goodies are listed in the target atlas spec file, and make
 sure you check the box that indicates atlas to individual.  Then, whatever
 you specify in the target atlas gets resampled into your source directory
 onto source mesh.

  For example, I would like to
  view the PHT parcellation on the individual surface (or at least have a
 label for each vertex so that I can view it in matlab).
 
  I would appreciate it if you find the time to provide some comments.
 
  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 

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 Macaque.LANDMARKS_for_FULL-HEM.bordercolor
and I think there is a good correspondence
between the individual and template LANDMARKS.

To perform the spherical registration however, I need the template sphere
of the left hemisphere, while I can only find the one of the
right hemisphere (Macaque.ATLAS.sphere.6.73730.coord). Do you know where I
can find it? (Maybe I can obtain it by mirroring, but
I have no idea how this could be done).

And I have a couple of general questions:

1. In which file-types are the sulcal-depths stored? (this applies both to
individual as well as template data)?  I quess this should be a
.surface_shape file, but I cannot find it. I ask this because I want to
make a new directory which only contains those files that I need.

2. In connection with this: What is the best way to organize the data
files? I now make different folders (one  for flattening, one for
landmarks, and one for the registration, each containing a different set of
data files and a single .spec file). Should I put everything
in one folder and make different .spec files for the different procedures?

3. Why are there .topology files? (since the topology is determined by the
triangulation, which is stored in .coord files)


4. After registering, how can I project any goodies defined on the template
to the individual surface? For example, I would like to
view the PHT parcellation on the individual surface (or at least have a
label for each vertex so that I can view it in matlab).

I would appreciate it if you find the time to provide some comments.

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 

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 
 Macaque.F99UA1.LR.AVERAGE.LANDMARKS_for_FULL-HEMISPHERE_RegWithPHT00.73730.borderproj
  with
 corresponding .bordercolor filee Macaque.LANDMARKS_for_FULL-HEM.bordercolor 
 and I think there is a good correspondence
 between the individual and template LANDMARKS.
 
 To perform the spherical registration however, I need the template sphere of 
 the left hemisphere, while I can only find the one of the
 right hemisphere (Macaque.ATLAS.sphere.6.73730.coord). Do you know where I 
 can find it? (Maybe I can obtain it by mirroring, but
 I have no idea how this could be done).

Use the right for both.  Caret with x-flip the left hems when it does its 
thing, provided the source spec file correctly identifies the hemisphere.

In this way, the resulting left and right hem resampled surfaces are in 
register with one another.

Just make sure there is a hemisphere tag that correctly identifies your left 
hem, and Caret will do the rest.

 And I have a couple of general questions:
 
 1. In which file-types are the sulcal-depths stored? (this applies both to 
 individual as well as template data)?  I quess this should be a
 .surface_shape file, but I cannot find it. I ask this because I want to make 
 a new directory which only contains those files that I need.

Should be surface_shape, but depending on what spec file you are using, you 
might not have one.  Or if it is more recent, it might be shape.gii.  The Sept 
2006 tutorial has a surface_shape for the macaque F99 in the MACAQUE subdir, 
for example.

If your individual was segmented in Caret, then it should have a sulcal depth 
map from the prepare for flattening step.  This should be in a surface shape 
file.  If you used something else, then are you sure you need the sulcal depth 
map?  If you just want something that looks like it for visualization, the 
Freesurfer .sulc is a good substitute.

 2. In connection with this: What is the best way to organize the data files? 
 I now make different folders (one  for flattening, one for
 landmarks, and one for the registration, each containing a different set of 
 data files and a single .spec file). Should I put everything
 in one folder and make different .spec files for the different procedures?

One hem, different specs.

 3. Why are there .topology files? (since the topology is determined by the 
 triangulation, which is stored in .coord files)

Coords contain only x,y,z coordinates.  Neighbor relationships are in the .topo 
files.

 4. After registering, how can I project any goodies defined on the template 
 to the individual surface?

Make sure the goodies are listed in the target atlas spec file, and make sure 
you check the box that indicates atlas to individual.  Then, whatever you 
specify in the target atlas gets resampled into your source directory onto 
source mesh.

 For example, I would like to
 view the PHT parcellation on the individual surface (or at least have a label 
 for each vertex so that I can view it in matlab).
 
 I would appreciate it if you find the time to provide some comments.
 
 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 

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 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 we also have a nifti extension for that, but it's
 not understood by other viewers.

 Caret5 has two volume formats that store that color lookup info:  AFNI,
 using a caret-specific header extension, and wustl's IFH/4dfp.  The ifh
 header lists the lookup, with an offset of 2.  (Like I said:  Messy.)  I
 can point you to some helpful threads on caret-users if needed.

  The background is that we want to construct a computational model of
 cortical dynamics using the structural connectivity information.
  An alternative, I guess, would be to spherically register the individual
 surface to the F99 template and subsequently, use the CoCoMAc
  or other available connectivity data. The drawback of this, however, is
 that the strength of connections is more or less qualitative, hence
  not so well-suited for modeling. If you think, though, that this is the
 best option for the creation of a surface-atlas, then I will go for it.

 See how far you get with the easy option.  If not far enough, 

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 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

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 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

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 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

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 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 

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 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 we also have a nifti extension for that, but it's not understood by 
other viewers.

Caret5 has two volume formats that store that color lookup info:  AFNI, using a 
caret-specific header extension, and wustl's IFH/4dfp.  The ifh header lists 
the lookup, with an offset of 2.  (Like I said:  Messy.)  I can point you to 
some helpful threads on caret-users if needed.

 The background is that we want to construct a computational model of cortical 
 dynamics using the structural connectivity information.
 An alternative, I guess, would be to spherically register the individual 
 surface to the F99 template and subsequently, use the CoCoMAc
 or other available connectivity data. The drawback of this, however, is that 
 the strength of connections is more or less qualitative, hence
 not so well-suited for modeling. If you think, though, that this is the best 
 option for the creation of a surface-atlas, then I will go for it.

See how far you get with the easy option.  If not far enough, then it's 
possible the McLaren atlas mesh is in register with F99.  I can't recall 
clearly, but read that link above for more info.

 Thanks a lot Donna, and kind regards,
 Rikkert
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker do...@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. Subsequently, I would like to use this atlas to get a parcellation 
  of the cortical surface of an individual macaque brain). How should I 
  approach this problem?
 
  I have extracted the cortical 

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 would like to use this atlas to get a parcellation of 
 the cortical surface of an individual macaque brain). How should I approach 
 this problem?
 
 I have extracted the cortical surface from the averaged T1-weigthed scan.  
 Should I now
 just label each cortical vertex by determining to which ROI it belongs? And 
 what if some vertices fall outside all ROI's? Also, the result does not look 
 so smooth as existing atlases.

It sounds like you need to map the volume(s) onto the surface.  It also sounds 
like these are discrete parcellations (ROI/label/paint) as opposed to 
probabilistic atlases, since it sounds like it is an individual monkey's data, 
rather than group data.  It would be helpful to clarify this.

Assuming it is ROI/label (i.e., each intensity value -- e.g., 1, 2, 3, … -- 
corresponds to a region -- e.g., cingulate, arcuate, …), then I would map it as 
a paint volume.  I believe doing so constrains the mapping algorithms, but I am 
not certain.

If you load your anatomical T1 with your surfaces and toggle on the surface 
contours (Volume Surface Outline, on the D/C page selection), then you can 
overlay the volumetric atlas over these two anatomical underlays (T1+surface 
contours) to look for regions where the surface does not intersect the atlas.  
I see three choices:

* fix the volumetric atlas data
* fix the surfaces, so the intersection is improved
* accept the fact that there are real holes in your data

You will be better equipped to make that choice when you are looking at 
T1+surface contours+volumetric-atlas.

 And to parcellate an individual macaque brain, can I register both the 
 surfaces (that is, the template surface and the individual surface) 
 spherically?

Registering an individual monkey brain to a monkey atlas (e.g., F99) isn't 
really parcellating it, but there are parcellations already on the F99 atlas, 
so if you use spherical registration to register your monkey to F99, then you 
could look at the F99 parcellations overlaid on your monkey's surface.  But 
it's not a quick or easy process.  You need to draw registration borders.  
(Though there are other registration algorithms out there that use sulcal maps 
and/or other data to automatically derive the deformation.  I encourage others 
to chime in if they ones they have used and found not too hard.)  How would you 
be using the registered surface?

(Sorry for the delayed reply, but it wasn't a quick one. ;-)

 Thanks a lot,
 Rikkert
 
 
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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
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.

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?
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?

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).

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)

The background is that we want to construct a computational model of
cortical dynamics using the structural connectivity information.
An alternative, I guess, would be to spherically register the individual
surface to the F99 template and subsequently, use the CoCoMAc
or other available connectivity data. The drawback of this, however, is
that the strength of connections is more or less qualitative, hence
not so well-suited for modeling. If you think, though, that this is the
best option for the creation of a surface-atlas, then I will go for it.


Thanks a lot Donna, and kind regards,
Rikkert














On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker do...@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. Subsequently, I would like to use this atlas to get a
 parcellation of the cortical surface of an individual macaque brain). How
 should I approach this problem?
 
  I have extracted the cortical surface from the averaged T1-weigthed
 scan.  Should I now
  just label each cortical vertex by determining to which ROI it belongs?
 And what if some vertices fall outside all ROI's? Also, the result does not
 look so smooth as existing atlases.

 It sounds like you need to map the volume(s) onto the surface.  It also
 sounds like these are discrete parcellations (ROI/label/paint) as opposed
 to probabilistic atlases, since it sounds like it is an individual monkey's
 data, rather than group data.  It would be helpful to clarify this.

 Assuming it is ROI/label (i.e., each intensity value -- e.g., 1, 2, 3, …
 -- corresponds to a region -- e.g., cingulate, arcuate, …), then I would
 map it as a paint volume.  I believe doing so constrains the mapping
 algorithms, but I am not certain.

 If you load your anatomical T1 with your surfaces and toggle on the
 surface contours (Volume Surface Outline, on the D/C page selection), then
 you can overlay the volumetric atlas over these two anatomical underlays
 (T1+surface contours) to look for regions where the surface does not
 intersect the atlas.  I see three choices:

 * fix the volumetric atlas data
 * fix the surfaces, so the intersection is improved
 * accept the fact that there are real holes in your data

 You will be better equipped to make that choice when you are looking at
 T1+surface contours+volumetric-atlas.

  And to parcellate an individual macaque brain, can I register both the
 surfaces (that is, the template surface and the individual surface)
 spherically?

 Registering an individual monkey brain to a monkey atlas (e.g., F99) isn't
 really parcellating it, but there are parcellations already on the F99
 atlas, so if you use spherical registration to register your monkey to F99,
 then you could look at the F99 parcellations overlaid on your monkey's
 surface.  But it's not a quick or easy process.  You need to draw
 registration borders.  (Though there are other registration algorithms out
 there that use sulcal maps and/or other data to automatically derive the
 deformation.  I encourage others to chime in if they ones they have used
 and found not too hard.)  How would you be using the registered surface?

 (Sorry for the delayed reply, but it wasn't a quick one. ;-)

  Thanks a lot,
  Rikkert
 
 
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