Hi Long, For the benefit of those on the list who did not see the off-list exchange with Alex, you are trying to use an individual's functional connectivity to detect his/her areal boundaries, similar to what Alex Cohen did in his Neuroimage paper last year. Note that this is a nontrivial undertaking. I think Steve Petersen said something like, "Our methods are elaborate." This isn't intended to discourage you; rather, it just makes clear that this process is neither quick nor easy.
I don't think using the PALS average fiducial surface is going to work for this purpose. You need to segment your subject's hemisphere and probably register it to PALS_B12 using surface-based registration. (Strictly speaking, you could get the ROI seed points without registering to PALS_B12; however, I believe doing so simplifies downstream steps.) If the fMRI data are normalized to MNI152, then the structural volume also should be, before segmenting. (You could also apply the normalization to the surface coordinates after the fact.) Once you have your individual segmented, you can create a flat map; generate cartesian grid; project borders; and save as border relative to your individual's fiducial surface (which is normalized to MNI152, since the original volume input to Caret was). Border points in that file will look like this: 0 0 -26.845331 -40.037304 -4.068827 0.000000 1 0 -28.127172 -39.991398 -5.601937 0.000000 2 0 -29.334217 -39.546257 -7.078649 0.000000 You'll need some external program (matlab script?) to read columns 3-5 above into 3D coordinates for your seed points. You'll need some software utility to create a sphere of specified radius around that point in volume-land. Alex probably uses one of Avi Snyder's programs to do this. AFNI may have something that does this. If not, I think perhaps you can write a script to do it in Caret. There are probably many options to do this. Then you use this volume that is all zeroes except for this sphere for your functional connectivity analysis. This is pretty much a black box to me. Good luck! Donna On 07/20/2009 09:53 AM, Long wrote: > 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] > <mailto:[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] <mailto:[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]> > <mailto:[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]>> > > > <mailto:[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]>> > > <mailto:[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]>> > > <mailto:[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> > (WORK Email) > > > [email protected] > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[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]>>> > > > <mailto:[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]>>> > > > >> > <mailto:[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] > <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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
