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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