[caret-users] How to export flatten image as a 2D image?
Long
longspace82 at gmail.com
Mon Jul 20 09:53:56 CDT 2009
p.s., the fMRI data are normalized by SPM5, and the template is MNI152.
That's why I always wonder if the border file is in T&T or MNI152 space. If
so, I can use the coordinates that stored in the fiducial border map as
ROIs.
On Mon, Jul 20, 2009 at 4:49 PM, Long <longspace82 at gmail.com> wrote:
> Dear Donna,
>
> Thank you for your help. My main purpose is to use the created border
> (white dots in former figures) as ROIs, and then use these ROIs to perform
> correlaton analysis in fMRI data. I think my current problem is how to
> convert the border data to the volume data, i.e. create the volume ROIs base
> on the fiducial or flat border file. Pleas help and sincerely looking
> forward to your reply.
>
> Best,
> Long
>
>
> On Fri, Jul 17, 2009 at 4:12 PM, Donna Dierker <donna at brainvis.wustl.edu>wrote:
>
>> Hi Long,
>>
>> This spec file has the AFNI fiducial coord file, specifically:
>>
>> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_AFNI.clean.73730.coord
>>
>> These are Talairach coordinates. There are several other versions of
>> the PALS fiducial coord file out there (and specifically in everyone's
>> caret/data_files/fmri_mapping_files subdirectory) that support
>> alternative stereotaxic spaces, like MNI152.
>>
>> But if you are using a volume that comes with Mricron, then I'd be
>> surprised if it were in Talairach space; I'd expected MNI152.
>>
>> The point is that you can't use a volume in MNI152 to sanity check the
>> alignment of data in Talairach space:
>>
>> http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
>>
>> Find out more about ch2.nii. I wish I had time to, but I don't.
>>
>> Donna
>>
>> On 07/16/2009 09:40 AM, Long wrote:
>> > Hi Donna,
>> >
>> > It's really appreciate for your detailed answer. I am using the
>> > FIDUCIAL surface of PALS_B12.RIGHT.MCW_2008_06.73730.spec, and
>> > creating border files as you taught me. So, is that the stereoscopic
>> > coordinates which stored in the FIDUCIAL surface border file are the
>> > Talairach coordinates? I just simply treat them as the Talairach
>> > coordinates at beginning. If not, how can I convert these data to the
>> > Talairach coordinates?
>> >
>> > Best,
>> > Long
>> >
>> > On Thu, Jul 16, 2009 at 2:50 PM, Donna Dierker
>> > <donna at brainvis.wustl.edu <mailto:donna at brainvis.wustl.edu>> wrote:
>> >
>> > Hi Long,
>> >
>> > See inline reply below.
>> >
>> > Donna
>> >
>> > On 07/16/2009 04:45 AM, Long wrote:
>> > > Hi,
>> > >
>> > > Also, I try to merge my modified border data, which inside the BA
>> 4,
>> > > on the FLATmap and FIDUCIAL map of
>> > > PALS_B12.RIGHT.MCW_2008_06.73730.spec, attached are the pics. I
>> > think
>> > > my question is due to the difference of BA temlate between
>> > Mricron and
>> > > Caret. Maybe I should trust one of them and I don't know which.
>> > >
>> > > Best,
>> > > Long
>> > >
>> > > On Wed, Jul 15, 2009 at 7:07 PM, Long <longspace82 at gmail.com
>> > <mailto:longspace82 at gmail.com>
>> > > <mailto:longspace82 at gmail.com <mailto:longspace82 at gmail.com>>>
>> > wrote:
>> > >
>> > > Many thanks to Donna and Alex! Now I begin to know the
>> > meaning of
>> > > border files and coord files.
>> > >
>> > > Recently, I tried to delineate the flat map with the border
>> > file.
>> > > I used PALS_B12.RIGHT.MCW_2008_06.73730.spec as a template.
>> > Then I
>> > > created a set of grid borders, which around the BA 4, and
>> > put the
>> > > FLAT border file into the Matlab. Then the flat map, which was
>> > > filled with dots, was delineated well in Matlab.
>> > >
>> > > I also export the border file of FIDUCIAL map.
>> > >
>> >
>> > Okay, the captures are very helpful in illustrating what you are
>> doing
>> > -- thanks.
>> >
>> > > Then I used these coordinates data which were stored in that
>> > > border file to create a 3D matrix, and export this 3D matrix
>> > as a
>> > > nifti file.
>> > >
>> >
>> > Whoa. If you want to export something as NIfTI, which I think of
>> > as 3D
>> > voxel grid -- not sparse 3D points -- then you should use the BA4
>> > paint
>> > and use Attributes: Paint: Convert paint column to paint volume.
>> > You'll
>> > end up with a slab of voxels, and the "space" will depend on
>> whatever
>> > fiducial surface you used. If you are using
>> > PALS_B12.RIGHT.MCW_2008_06.73730.spec, there is a good chance the
>> > default fiducial coord file is AFNI, which is considerably smaller
>> > than
>> > the MNI options (FLIRT, MRITOTAL, SPM*).
>> >
>> > I suppose if you do somehow use matlab to write the border points as
>> > NIfTI, then be mindful of which fiducial surface you use when
>> > saving the
>> > fiducial border file. Here are some useful documents:
>> >
>> > http://brainvis.wustl.edu/help/pals_volume_normalization/
>> > http://dx.doi.org/10.1016/j.neuroimage.2007.02.021
>> >
>> > > However, when I merge this nifti image on the ch2.hii.gz
>> > (provided
>> > > by Mricron), the voxels of this 'BA4 border' image were not
>> > > located around BA 4, and almost of them were located at BA 6.
>> I
>> > > also try converting the coordinates data into MNI
>> > coordinates, but
>> > > the voxels still not around the BA 4.
>> > >
>> >
>> > I am unfamiliar with ch2.hii.gz. Hypothetically, let's say it is
>> some
>> > population template in MNI152 space (may not be). Then try saving
>> the
>> > border points (or Attributes: Paint: Convert paint column to paint
>> > volume) using the FLIRT or SPM* fiducials surfaces, and see if your
>> > results look more sane.
>> >
>> > >
>> > > Therefore, how can I create a correct 3D image with the border
>> > > file of FIDUCIAL map?
>> > >
>> > The procedure you are using to convert border points to voxels is a
>> > black box to me, so the problem could lie there. But it could be as
>> > simple as using the wrong reference fiducial surface when saving
>> your
>> > fiducial borders.
>> >
>> > >
>> > > Thanks for your help.
>> > > Long
>> > >
>> > > On Thu, Jul 9, 2009 at 11:05 PM, Alexander Li Cohen
>> > > <alexc at npg.wustl.edu <mailto:alexc at npg.wustl.edu>
>> > <mailto:alexc at npg.wustl.edu <mailto:alexc at npg.wustl.edu>>> wrote:
>> > >
>> > > Yes,
>> > > as Donna stated, the 'generated Cartesian analysis
>> > grid' is the
>> > > Caret function I asked John to add so we could generate 2D
>> > > cartesian
>> > > grids on a flat surface, and then project the border so
>> it's
>> > > folded
>> > > onto the fiducial surface... it IS a distorted grid (due
>> > to the
>> > > flattening), but dealing with a triangulated mesh in 2d,
>> or
>> > > otherwise,
>> > > is much more difficult for me to visualize (not that it
>> > can't be
>> > > done... someday I hope to move towards that...) The
>> > subsequent
>> > > steps
>> > > are done in matlab and standard fMRI processing tools,
>> with
>> > > occasional
>> > > use of caret_command to convert to and from surfaces if
>> > needed...
>> > >
>> > > transitioning to the sphere is in development, but of
>> > course,
>> > > it's a
>> > > lot harder and we're still working on it...
>> > >
>> > > -Alex
>> > > ~)---------------
>> > >
>> > >
>> >
>> ----------------------------------------------------------------------
>> > > Alexander Li Cohen
>> > > alexc at npg.wustl.edu <mailto:alexc at npg.wustl.edu>
>> > <mailto:alexc at npg.wustl.edu <mailto:alexc at npg.wustl.edu>> (WORK
>> Email)
>> > > alexcohen at gmail.com <mailto:alexcohen at gmail.com>
>> > <mailto:alexcohen at gmail.com <mailto:alexcohen at gmail.com>>
>> > (Non-secure /
>> > > rapid-response Email)
>> > > Petersen/Schlaggar Lab
>> > > Medical Scientist Training Program
>> > > Washington University in St. Louis School of Medicine
>> > >
>> >
>> ----------------------------------------------------------------------
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>> > >
>> > > On Jul 9, 2009, at 2:09 PM, Donna Dierker wrote:
>> > >
>> > > > Hi Long,
>> > > >
>> > > > Oh, okay. You mean this paper, where Alex detects areal
>> > > boundaries
>> > > > using functional connectivity:
>> > > >
>> > > > http://dx.doi.org/10.1016/j.neuroimage.2008.01.066
>> > > >
>> > > > This is a legitimate use of a flat map, although I think
>> > > that Alex
>> > > > Cohen
>> > > > may have figured out a way of using the spherical map,
>> > > instead. Over
>> > > > time, he has simplified this process. Alex is a
>> > caret-users
>> > > > subscriber,
>> > > > but I forward this reply to him, to make sure he sees
>> it.
>> > > >
>> > > > The activation map for each subject is generated in
>> > volume-land.
>> > > > The 2D
>> > > > image analysis (edge detection, etc.) is better
>> > answered by Alex
>> > > > directly.
>> > > >
>> > > > But let me describe one way you could create the seeds:
>> > > >
>> > > > 1. Load flat map in main Caret window. Load fiducial
>> > > surface in
>> > > > Window 2.
>> > > >
>> > > > 2. Select Layers: Borders: Create Cartesian Grid Flat
>> > > borders and
>> > > > enter
>> > > > the desired spacing.
>> > > >
>> > > > 3. Select Layers: Borders: Project borders.
>> > > >
>> > > > 4. Select File: Save Data File: Border Files - Surface:
>> > > Associated
>> > > > surface -- change from Flat to Fiducial.
>> > > >
>> > > > The resulting border file can be opened in a text editor
>> > > and/or read
>> > > > in
>> > > > by a program like Matlab. It contains a bunch of border
>> > > points that
>> > > > represent this grid on the flat map projected onto the
>> > > fiducial --
>> > > > i.e.,
>> > > > the grid all crumpled up the way the cortex actually is.
>> > > Like I said,
>> > > > it is possible Alex is doing this on the PALS_B12
>> > sphere now
>> > > (using
>> > > > fiducial surfaces that have been resampled to the
>> standard
>> > > mesh, but
>> > > > still look pretty much identical to the native mesh
>> > ones in
>> > > geometry).
>> > > >
>> > > > At any rate, there is no need to capture the flat map
>> > as an
>> > > image, nor
>> > > > any involvement with the Brodmann parcellation
>> whatsoever.
>> > > On the
>> > > > contrary, if you do what Alex does, it is probably
>> INSTEAD
>> > > OF Brodmann
>> > > > areas (although it would be fun to compare).
>> > > >
>> > > > Donna
>> > > >
>> > > > On 07/09/2009 09:35 AM, Long wrote:
>> > > >> Dear Donna,
>> > > >>
>> > > >> Thank you for your quickly reply. My main purpose is to
>> > > analyze the
>> > > >> cerebral cortex by using fMRI data in 2D way. Just like
>> > > your group
>> > > >> did
>> > > >> in paper: Defining functional areas in individual human
>> > > brains using
>> > > >> resting functional connectivity MRI. Neuroimage.
>> > 2008. How
>> > > to create
>> > > >> seeds and after calculating, how to create a
>> 'activation
>> > > map' on a
>> > > >> flatten cortex and perform the 2D image analysis.
>> > > >>
>> > > >> Thanks for your help.
>> > > >> Long
>> > > >>
>> > > >> On Thu, Jul 9, 2009 at 3:05 PM, Donna Dierker
>> > > >> <donna at brainvis.wustl.edu
>> > <mailto:donna at brainvis.wustl.edu> <mailto:donna at brainvis.wustl.edu
>> > <mailto:donna at brainvis.wustl.edu>>
>> > > <mailto:donna at brainvis.wustl.edu
>> > <mailto:donna at brainvis.wustl.edu>
>> > > <mailto:donna at brainvis.wustl.edu
>> > <mailto:donna at brainvis.wustl.edu>>>> wrote:
>> > > >>
>> > > >> On 07/09/2009 06:30 AM, Long wrote:
>> > > >>
>> > > >> Dear caret-users,
>> > > >>
>> > > >> I want to analyze the flatten image as a 2D
>> image,
>> > > so there
>> > > >> are a series of questions about this:
>> > > >>
>> > > >> 1) How to export a flatten cortex as a 2D
>> > image? So
>> > > I can use
>> > > >> some 2D image processing methods.
>> > > >>
>> > > >> I might misunderstand you, but I think it is as
>> > simple as
>> > > >> displaying the flat map in the main Caret window and
>> > > doing File:
>> > > >> Capture Image of Window.
>> > > >>
>> > > >>
>> > > >> 2) If a cortex was flattened, how to use the new
>> > > reference
>> > > >> coordinate system in 2D cortex to identify the
>> 3D
>> > > coordinates,
>> > > >> e.g., MNI coordinates?
>> > > >>
>> > > >> In Caret, one typically would have a single topology
>> > > file for all
>> > > >> "CLOSED" surface configurations (e.g.,
>> > > fiducial/midthickness;
>> > > >> inflated; spherical), and a CUT topology file for
>> any
>> > > flat ones.
>> > > >> The topology files store the neighbor relationships
>> > > between the
>> > > >> nodes, so you can see why a flat surface, which has
>> > > cuts, would
>> > > >> differ in its neighbors from a surface with no cuts,
>> > > like the
>> > > >> midthickness. But each of these different
>> > configurations --
>> > > >> fiducial, inflated, spherical, flat -- has its own
>> > > coordinate
>> > > >> (.coord) file. By default, Caret writes these coord
>> > > files as
>> > > >> binary; however, you can change the default to
>> > write them as
>> > > >> ASCII, so you can read in the coords into Matlab
>> > or whatever
>> > > >> software you like.
>> > > >>
>> > > >> If written in ASCII, the coord file will always
>> > have the
>> > > node
>> > > >> number in the first column, so you can grep or
>> > join the
>> > > 2D (flat
>> > > >> coord) and 3D (fiducial coord) files by the node
>> > number.
>> > > See
>> > > >>
>> > >
>> >
>> http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile
>> > > >> for more information about the coord file format.
>> > > >>
>> > > >> What is the relationship between 2D and 3D
>> cortex.
>> > > >>
>> > > >> It is not a simple one, like an equation. Besides
>> 2D
>> > > having cuts
>> > > >> (broken neighbor relationships), the nodes have been
>> > > projected
>> > > >> onto a Z=0 plane and then morphed across five
>> > cycles to
>> > > reduce
>> > > >> distortion and crossovers. But the node
>> > correspondence
>> > > remains
>> > > >> the same across configurations.
>> > > >>
>> > > >> It seems like you might want to do something like
>> > this:
>> > > >>
>> > > >> 1. click on the 2D image
>> > > >> 2. find the closest node on the 2D coord
>> > > >> 3. lookup up the corresponding 3D coordinate in the
>> > > fiducial coord
>> > > >>
>> > > >> This is easy in Caret, and if you have flat
>> > surface in main
>> > > >> window, fiducial in window 2, Caret will print the
>> > > fiducial 3D
>> > > >> coordinate in the ID window whenever you click on
>> > a node
>> > > in the
>> > > >> flat surface (main window).
>> > > >>
>> > > >> But once you export the flat to a 2D image, rather
>> > than
>> > > remain in
>> > > >> Caret, which is node-aware, you will have trouble
>> > > getting from
>> > > >> step 1 to step 2 above.
>> > > >>
>> > > >>
>> > > >> 3) How to export one or two flatten Brodmann
>> areas
>> > > based on
>> > > >> the Brodmann template as a 2D image?
>> > > >>
>> > > >> This requires registering your individual subjects
>> to
>> > > the PALS_B12
>> > > >> atlas, so you can deform the atlas Brodmann paint
>> file
>> > > to your
>> > > >> subjects' flat maps. Alternatively, you can
>> > deform any
>> > > measure of
>> > > >> interest from your subjects to the PALS_B12 atlas,
>> and
>> > > look at the
>> > > >> Brodmann regions on the atlas flat map, which has
>> > a standard
>> > > >> shape/outline (see attached capture).
>> > > >>
>> > > >> Be aware of distortions in the flat maps --
>> > compression
>> > > near the
>> > > >> center, expansion at the edges. We tend NOT to
>> > use them for
>> > > >> measurement/statistical purposes; rather, they are
>> > handy for
>> > > >> drawing borders and displaying an image of the
>> entire
>> > > cortex in
>> > > >> one view. I wonder how you will be using them.
>> > > >>
>> > > >>
>> > > >> Thanks for your help.
>> > > >> Long
>> > > >>
>> > > >>
>> > >
>> >
>> ------------------------------------------------------------------------
>> > > >>
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