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 <[email protected]> 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 > <[email protected]>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 >> > <[email protected] <mailto:[email protected]>> 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 <[email protected] >> > <mailto:[email protected]> >> > > <mailto:[email protected] <mailto:[email protected]>>> >> > 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 >> > > <[email protected] <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>>> 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 >> > > [email protected] <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>> (WORK >> Email) >> > > [email protected] <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>> >> > (Non-secure / >> > > rapid-response Email) >> > > Petersen/Schlaggar Lab >> > > Medical Scientist Training Program >> > > Washington University in St. Louis School of Medicine >> > > >> > >> ---------------------------------------------------------------------- >> > > >> > > This message is intended only for the exclusive use of the >> > > intended >> > > recipient(s) named herein and may contain information >> > that is >> > > PRIVILEGED and/or >> > > CONFIDENTIAL. If you are not the intended recipient, >> > you are >> > > hereby >> > > notified >> > > that any use, dissemination, disclosure or copying of this >> > > communication is >> > > strictly prohibited. If you have received this >> > communication in >> > > error, please >> > > destroy all copies of this message and its attachments and >> > > notify us >> > > immediately. >> > > >> > > The materials in this message are private and may contain >> > > Protected >> > > Healthcare Information or other information of a sensitive >> > > nature. If >> > > you are not the intended recipient, be advised that any >> > > unauthorized >> > > use, disclosure, copying or the taking of any action in >> > > reliance on >> > > the contents of this information is strictly prohibited. >> If >> > > you have >> > > received this email in error, please immediately notify >> the >> > > sender via >> > > telephone or return mail. >> > > >> > > 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 >> > > >> <[email protected] >> > <mailto:[email protected]> <mailto:[email protected] >> > <mailto:[email protected]>> >> > > <mailto:[email protected] >> > <mailto:[email protected]> >> > > <mailto:[email protected] >> > <mailto:[email protected]>>>> 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 >> > > >> >> > > >> >> > > >> > >> ------------------------------------------------------------------------ >> > > >> >> > > >> _______________________________________________ >> > > >> caret-users mailing list >> > > >> [email protected] >> > <mailto:[email protected]> >> > > <mailto:[email protected] >> > <mailto:[email protected]>> >> > > >> <mailto:[email protected] >> > <mailto:[email protected]> >> > > <mailto:[email protected] >> > <mailto:[email protected]>>> >> > > >> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >
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