[caret-users] How to export flatten image as a 2D image?
Long
longspace82 at gmail.com
Thu Jul 16 04:45:44 CDT 2009
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> 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. 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. 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.
>
> Therefore, how can I create a correct 3D image with the border file of
> FIDUCIAL map?
>
> Thanks for your help.
> Long
>
> On Thu, Jul 9, 2009 at 11:05 PM, Alexander Li Cohen <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 (WORK Email)
>> 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>> 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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>> >>
>> >>
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