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
