Hi Donna,<br><br>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?<br>
<br>Best,<br>Long<br><br><div class="gmail_quote">On Thu, Jul 16, 2009 at 2:50 PM, Donna Dierker <span dir="ltr"><<a href="mailto:donna@brainvis.wustl.edu">donna@brainvis.wustl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Long,<br>
<br>
See inline reply below.<br>
<br>
Donna<br>
<div class="im"><br>
On 07/16/2009 04:45 AM, Long wrote:<br>
> Hi,<br>
><br>
> Also, I try to merge my modified border data, which inside the BA 4,<br>
> on the FLATmap and FIDUCIAL map of<br>
> PALS_B12.RIGHT.MCW_2008_06.73730.spec, attached are the pics. I think<br>
> my question is due to the difference of BA temlate between Mricron and<br>
> Caret. Maybe I should trust one of them and I don't know which.<br>
><br>
> Best,<br>
> Long<br>
><br>
> On Wed, Jul 15, 2009 at 7:07 PM, Long <<a href="mailto:longspace82@gmail.com">longspace82@gmail.com</a><br>
</div><div class="im">> <mailto:<a href="mailto:longspace82@gmail.com">longspace82@gmail.com</a>>> wrote:<br>
><br>
> Many thanks to Donna and Alex! Now I begin to know the meaning of<br>
> border files and coord files.<br>
><br>
> Recently, I tried to delineate the flat map with the border file.<br>
> I used PALS_B12.RIGHT.MCW_2008_06.73730.spec as a template. Then I<br>
> created a set of grid borders, which around the BA 4, and put the<br>
> FLAT border file into the Matlab. Then the flat map, which was<br>
> filled with dots, was delineated well in Matlab.<br>
><br>
> I also export the border file of FIDUCIAL map.<br>
><br>
<br>
</div>Okay, the captures are very helpful in illustrating what you are doing<br>
-- thanks.<br>
<div class="im"><br>
> Then I used these coordinates data which were stored in that<br>
> border file to create a 3D matrix, and export this 3D matrix as a<br>
> nifti file.<br>
><br>
<br>
</div>Whoa. If you want to export something as NIfTI, which I think of as 3D<br>
voxel grid -- not sparse 3D points -- then you should use the BA4 paint<br>
and use Attributes: Paint: Convert paint column to paint volume. You'll<br>
end up with a slab of voxels, and the "space" will depend on whatever<br>
fiducial surface you used. If you are using<br>
PALS_B12.RIGHT.MCW_2008_06.73730.spec, there is a good chance the<br>
default fiducial coord file is AFNI, which is considerably smaller than<br>
the MNI options (FLIRT, MRITOTAL, SPM*).<br>
<br>
I suppose if you do somehow use matlab to write the border points as<br>
NIfTI, then be mindful of which fiducial surface you use when saving the<br>
fiducial border file. Here are some useful documents:<br>
<br>
<a href="http://brainvis.wustl.edu/help/pals_volume_normalization/" target="_blank">http://brainvis.wustl.edu/help/pals_volume_normalization/</a><br>
<a href="http://dx.doi.org/10.1016/j.neuroimage.2007.02.021" target="_blank">http://dx.doi.org/10.1016/j.neuroimage.2007.02.021</a><br>
<div class="im"><br>
> However, when I merge this nifti image on the ch2.hii.gz (provided<br>
> by Mricron), the voxels of this 'BA4 border' image were not<br>
> located around BA 4, and almost of them were located at BA 6. I<br>
> also try converting the coordinates data into MNI coordinates, but<br>
> the voxels still not around the BA 4.<br>
><br>
<br>
</div>I am unfamiliar with ch2.hii.gz. Hypothetically, let's say it is some<br>
population template in MNI152 space (may not be). Then try saving the<br>
border points (or Attributes: Paint: Convert paint column to paint<br>
volume) using the FLIRT or SPM* fiducials surfaces, and see if your<br>
results look more sane.<br>
<div class="im"><br>
><br>
> Therefore, how can I create a correct 3D image with the border<br>
> file of FIDUCIAL map?<br>
><br>
</div>The procedure you are using to convert border points to voxels is a<br>
black box to me, so the problem could lie there. But it could be as<br>
simple as using the wrong reference fiducial surface when saving your<br>
fiducial borders.<br>
<div class="im"><br>
><br>
> Thanks for your help.<br>
> Long<br>
><br>
> On Thu, Jul 9, 2009 at 11:05 PM, Alexander Li Cohen<br>
</div><div class="im">> <<a href="mailto:alexc@npg.wustl.edu">alexc@npg.wustl.edu</a> <mailto:<a href="mailto:alexc@npg.wustl.edu">alexc@npg.wustl.edu</a>>> wrote:<br>
><br>
> Yes,<br>
> as Donna stated, the 'generated Cartesian analysis grid' is the<br>
> Caret function I asked John to add so we could generate 2D<br>
> cartesian<br>
> grids on a flat surface, and then project the border so it's<br>
> folded<br>
> onto the fiducial surface... it IS a distorted grid (due to the<br>
> flattening), but dealing with a triangulated mesh in 2d, or<br>
> otherwise,<br>
> is much more difficult for me to visualize (not that it can't be<br>
> done... someday I hope to move towards that...) The subsequent<br>
> steps<br>
> are done in matlab and standard fMRI processing tools, with<br>
> occasional<br>
> use of caret_command to convert to and from surfaces if needed...<br>
><br>
> transitioning to the sphere is in development, but of course,<br>
> it's a<br>
> lot harder and we're still working on it...<br>
><br>
> -Alex<br>
> ~)---------------<br>
><br>
> ----------------------------------------------------------------------<br>
> Alexander Li Cohen<br>
</div>> <a href="mailto:alexc@npg.wustl.edu">alexc@npg.wustl.edu</a> <mailto:<a href="mailto:alexc@npg.wustl.edu">alexc@npg.wustl.edu</a>> (WORK Email)<br>
> <a href="mailto:alexcohen@gmail.com">alexcohen@gmail.com</a> <mailto:<a href="mailto:alexcohen@gmail.com">alexcohen@gmail.com</a>> (Non-secure /<br>
<div><div></div><div class="h5">> rapid-response Email)<br>
> Petersen/Schlaggar Lab<br>
> Medical Scientist Training Program<br>
> Washington University in St. Louis School of Medicine<br>
> ----------------------------------------------------------------------<br>
><br>
> This message is intended only for the exclusive use of the<br>
> intended<br>
> recipient(s) named herein and may contain information that is<br>
> PRIVILEGED and/or<br>
> CONFIDENTIAL. If you are not the intended recipient, you are<br>
> hereby<br>
> notified<br>
> that any use, dissemination, disclosure or copying of this<br>
> communication is<br>
> strictly prohibited. If you have received this communication in<br>
> error, please<br>
> destroy all copies of this message and its attachments and<br>
> notify us<br>
> immediately.<br>
><br>
> The materials in this message are private and may contain<br>
> Protected<br>
> Healthcare Information or other information of a sensitive<br>
> nature. If<br>
> you are not the intended recipient, be advised that any<br>
> unauthorized<br>
> use, disclosure, copying or the taking of any action in<br>
> reliance on<br>
> the contents of this information is strictly prohibited. If<br>
> you have<br>
> received this email in error, please immediately notify the<br>
> sender via<br>
> telephone or return mail.<br>
><br>
> On Jul 9, 2009, at 2:09 PM, Donna Dierker wrote:<br>
><br>
> > Hi Long,<br>
> ><br>
> > Oh, okay. You mean this paper, where Alex detects areal<br>
> boundaries<br>
> > using functional connectivity:<br>
> ><br>
> > <a href="http://dx.doi.org/10.1016/j.neuroimage.2008.01.066" target="_blank">http://dx.doi.org/10.1016/j.neuroimage.2008.01.066</a><br>
> ><br>
> > This is a legitimate use of a flat map, although I think<br>
> that Alex<br>
> > Cohen<br>
> > may have figured out a way of using the spherical map,<br>
> instead. Over<br>
> > time, he has simplified this process. Alex is a caret-users<br>
> > subscriber,<br>
> > but I forward this reply to him, to make sure he sees it.<br>
> ><br>
> > The activation map for each subject is generated in volume-land.<br>
> > The 2D<br>
> > image analysis (edge detection, etc.) is better answered by Alex<br>
> > directly.<br>
> ><br>
> > But let me describe one way you could create the seeds:<br>
> ><br>
> > 1. Load flat map in main Caret window. Load fiducial<br>
> surface in<br>
> > Window 2.<br>
> ><br>
> > 2. Select Layers: Borders: Create Cartesian Grid Flat<br>
> borders and<br>
> > enter<br>
> > the desired spacing.<br>
> ><br>
> > 3. Select Layers: Borders: Project borders.<br>
> ><br>
> > 4. Select File: Save Data File: Border Files - Surface:<br>
> Associated<br>
> > surface -- change from Flat to Fiducial.<br>
> ><br>
> > The resulting border file can be opened in a text editor<br>
> and/or read<br>
> > in<br>
> > by a program like Matlab. It contains a bunch of border<br>
> points that<br>
> > represent this grid on the flat map projected onto the<br>
> fiducial --<br>
> > i.e.,<br>
> > the grid all crumpled up the way the cortex actually is.<br>
> Like I said,<br>
> > it is possible Alex is doing this on the PALS_B12 sphere now<br>
> (using<br>
> > fiducial surfaces that have been resampled to the standard<br>
> mesh, but<br>
> > still look pretty much identical to the native mesh ones in<br>
> geometry).<br>
> ><br>
> > At any rate, there is no need to capture the flat map as an<br>
> image, nor<br>
> > any involvement with the Brodmann parcellation whatsoever.<br>
> On the<br>
> > contrary, if you do what Alex does, it is probably INSTEAD<br>
> OF Brodmann<br>
> > areas (although it would be fun to compare).<br>
> ><br>
> > Donna<br>
> ><br>
> > On 07/09/2009 09:35 AM, Long wrote:<br>
> >> Dear Donna,<br>
> >><br>
> >> Thank you for your quickly reply. My main purpose is to<br>
> analyze the<br>
> >> cerebral cortex by using fMRI data in 2D way. Just like<br>
> your group<br>
> >> did<br>
> >> in paper: Defining functional areas in individual human<br>
> brains using<br>
> >> resting functional connectivity MRI. Neuroimage. 2008. How<br>
> to create<br>
> >> seeds and after calculating, how to create a 'activation<br>
> map' on a<br>
> >> flatten cortex and perform the 2D image analysis.<br>
> >><br>
> >> Thanks for your help.<br>
> >> Long<br>
> >><br>
> >> On Thu, Jul 9, 2009 at 3:05 PM, Donna Dierker<br>
> >> <<a href="mailto:donna@brainvis.wustl.edu">donna@brainvis.wustl.edu</a> <mailto:<a href="mailto:donna@brainvis.wustl.edu">donna@brainvis.wustl.edu</a>><br>
> <mailto:<a href="mailto:donna@brainvis.wustl.edu">donna@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:donna@brainvis.wustl.edu">donna@brainvis.wustl.edu</a>>>> wrote:<br>
> >><br>
> >> On 07/09/2009 06:30 AM, Long wrote:<br>
> >><br>
> >> Dear caret-users,<br>
> >><br>
> >> I want to analyze the flatten image as a 2D image,<br>
> so there<br>
> >> are a series of questions about this:<br>
> >><br>
> >> 1) How to export a flatten cortex as a 2D image? So<br>
> I can use<br>
> >> some 2D image processing methods.<br>
> >><br>
> >> I might misunderstand you, but I think it is as simple as<br>
> >> displaying the flat map in the main Caret window and<br>
> doing File:<br>
> >> Capture Image of Window.<br>
> >><br>
> >><br>
> >> 2) If a cortex was flattened, how to use the new<br>
> reference<br>
> >> coordinate system in 2D cortex to identify the 3D<br>
> coordinates,<br>
> >> e.g., MNI coordinates?<br>
> >><br>
> >> In Caret, one typically would have a single topology<br>
> file for all<br>
> >> "CLOSED" surface configurations (e.g.,<br>
> fiducial/midthickness;<br>
> >> inflated; spherical), and a CUT topology file for any<br>
> flat ones.<br>
> >> The topology files store the neighbor relationships<br>
> between the<br>
> >> nodes, so you can see why a flat surface, which has<br>
> cuts, would<br>
> >> differ in its neighbors from a surface with no cuts,<br>
> like the<br>
> >> midthickness. But each of these different configurations --<br>
> >> fiducial, inflated, spherical, flat -- has its own<br>
> coordinate<br>
> >> (.coord) file. By default, Caret writes these coord<br>
> files as<br>
> >> binary; however, you can change the default to write them as<br>
> >> ASCII, so you can read in the coords into Matlab or whatever<br>
> >> software you like.<br>
> >><br>
> >> If written in ASCII, the coord file will always have the<br>
> node<br>
> >> number in the first column, so you can grep or join the<br>
> 2D (flat<br>
> >> coord) and 3D (fiducial coord) files by the node number.<br>
> See<br>
> >><br>
> <a href="http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile" target="_blank">http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile</a><br>
> >> for more information about the coord file format.<br>
> >><br>
> >> What is the relationship between 2D and 3D cortex.<br>
> >><br>
> >> It is not a simple one, like an equation. Besides 2D<br>
> having cuts<br>
> >> (broken neighbor relationships), the nodes have been<br>
> projected<br>
> >> onto a Z=0 plane and then morphed across five cycles to<br>
> reduce<br>
> >> distortion and crossovers. But the node correspondence<br>
> remains<br>
> >> the same across configurations.<br>
> >><br>
> >> It seems like you might want to do something like this:<br>
> >><br>
> >> 1. click on the 2D image<br>
> >> 2. find the closest node on the 2D coord<br>
> >> 3. lookup up the corresponding 3D coordinate in the<br>
> fiducial coord<br>
> >><br>
> >> This is easy in Caret, and if you have flat surface in main<br>
> >> window, fiducial in window 2, Caret will print the<br>
> fiducial 3D<br>
> >> coordinate in the ID window whenever you click on a node<br>
> in the<br>
> >> flat surface (main window).<br>
> >><br>
> >> But once you export the flat to a 2D image, rather than<br>
> remain in<br>
> >> Caret, which is node-aware, you will have trouble<br>
> getting from<br>
> >> step 1 to step 2 above.<br>
> >><br>
> >><br>
> >> 3) How to export one or two flatten Brodmann areas<br>
> based on<br>
> >> the Brodmann template as a 2D image?<br>
> >><br>
> >> This requires registering your individual subjects to<br>
> the PALS_B12<br>
> >> atlas, so you can deform the atlas Brodmann paint file<br>
> to your<br>
> >> subjects' flat maps. Alternatively, you can deform any<br>
> measure of<br>
> >> interest from your subjects to the PALS_B12 atlas, and<br>
> look at the<br>
> >> Brodmann regions on the atlas flat map, which has a standard<br>
> >> shape/outline (see attached capture).<br>
> >><br>
> >> Be aware of distortions in the flat maps -- compression<br>
> near the<br>
> >> center, expansion at the edges. We tend NOT to use them for<br>
> >> measurement/statistical purposes; rather, they are handy for<br>
> >> drawing borders and displaying an image of the entire<br>
> cortex in<br>
> >> one view. I wonder how you will be using them.<br>
> >><br>
> >><br>
> >> Thanks for your help.<br>
> >> Long<br>
> >><br>
> >><br>
> ------------------------------------------------------------------------<br>
> >><br>
> >> _______________________________________________<br>
> >> caret-users mailing list<br>
> >> <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> >> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>>><br>
> >> <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
> >><br>
> >><br>
> >><br>
> >><br>
> >> _______________________________________________<br>
> >> caret-users mailing list<br>
> >> <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> >> ><br>
> >> <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
> >><br>
> >><br>
> >><br>
> ------------------------------------------------------------------------<br>
> >><br>
> >> _______________________________________________<br>
> >> caret-users mailing list<br>
> >> <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> >> <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
> >><br>
> ><br>
> > _______________________________________________<br>
> > caret-users mailing list<br>
> > <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> > <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
><br>
> _______________________________________________<br>
> caret-users mailing list<br>
> <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <mailto:<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a>><br>
> <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
><br>
><br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> caret-users mailing list<br>
> <a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
> <a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
><br>
<br>
_______________________________________________<br>
caret-users mailing list<br>
<a href="mailto:caret-users@brainvis.wustl.edu">caret-users@brainvis.wustl.edu</a><br>
<a href="http://brainvis.wustl.edu/mailman/listinfo/caret-users" target="_blank">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a><br>
</div></div></blockquote></div><br>