Surfaces were generated in undistorted native volume space rigidly rotated to roughly align with MNI space.
One can use affine or nonlinear warp fields to transform coordinates just as one can transform images. It is just with coordinates one’s precision is much higher because coordinates are floats, whereas images have to be sampled onto a grid. Peace, Matt. On 3/27/15, 2:24 PM, "Liu, Zhongming" <[email protected]> wrote: >Thanks Matt for your prompt and patient replies to all the questions. >Unbelievable amount and quality of your work. > >What exactly do you mean by volume transformation of surface coordinates? > >Was the surface generated by the anatomical images in the MNI space or >the native space? > >Zhongming > >Sent from my iPhone > >> On Mar 27, 2015, at 2:23 PM, Glasser, Matthew <[email protected]> >>wrote: >> >> So we had a thread about this a few weeks back. Surface registration >>and >> volume registration are two completely independent things, so long as >>the >> surfaces are originally created in native subject space. We don’t do it >> way #1 because that would require making two large volume timeseries and >> we want to avoid as many operations on volume timeseries of high spatial >> and temporal resolution data as possible because they are >>computationally >> extremely expensive. Volume transformations of surface coordinates are >> exact (no interpolation to a grid), so the individual surface still >>lines >> up exactly with the fMRI timeseries in MNI space. There is a 3rd way >>that >> could have been used at greater complication and computational expense >> (see the past thread for details) but even less interpolation, and if >> someone wants to code it up, we’d consider accepting the patch. ;) >> >> Peace, >> >> Matt. >> >>> On 3/27/15, 1:18 PM, "Liu, Zhongming" <[email protected]> wrote: >>> >>> Matt: >>> >>> I am also uncertain what was done when creating the surface >>> representation of fMRI time series data. >>> >>> Which of the following (or other) ways are done? >>> 1) volume time series in native space -> volume-to-surface mapping onto >>> the cortical surface in native space -> >>> native-surface-to-MNI-surface-template registration >>> 2) volume time series in MNI space -> volume-to-surface mapping onto >>>the >>> cortical surface in MNI space, while the surface is still specific to >>> each individual -> MNI-surface-to-MNI-surface-template registration >>> >>> If 1) is done, then one does not need to do anything in order to get >>> volume time series data in MNI. >>> If 2) is done, then is it true that the potential inaccuracy of >>> non-linear registration, interpolation, etc will still be of concern >>>and >>> potentially defeat the purpose of acquiring data with high resolution? >>> >>> Reading your NeuroImage_2013 paper, it looks like that 2) is being done >>> in the HCP pipeline. >>> >>> Zhongming >>> >>>> On Mar 27, 2015, at 12:44 PM, Glasser, Matthew >>>> <[email protected]> wrote: >>>> >>>> That will depend on the surface you choose to use, as the cortical >>>> grayordinates are particular surface vertices on a standard surface >>>>mesh >>>> topology. The 3D volume coordinates of these vertices can change >>>>across >>>> subjects, but cross-subject correspondence is maintained through >>>>having >>>> the same vertex number mean the same anatomical location in each >>>> subject. >>>> Perhaps you can give me some more details on what you are doing and I >>>> can >>>> be more helpful then. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>>> On 3/27/15, 11:25 AM, "Alpay Özcan" <[email protected]> wrote: >>>>> >>>>> Matt, >>>>> thank you for your quick reply. >>>>> >>>>> Just to clarify, my original question was not implying anything >>>>> negative about the grayordinates nor any desire to work in MNI space. >>>>> In fact, in my view, grayordinates are logically addressing many >>>>>space >>>>> constraints and analysis problems appropriately. >>>>> >>>>> To rephrase the question, I would like to obtain the definition >>>>> of the grayordinates in 91x109x91 volume. The description does not >>>>>need >>>>> to be in the form of a matrix, e.g., a coordinate translation map >>>>>would >>>>> do. For example (I am making up the numbers): >>>>> >>>>> 42,50,50 ---> 1st entry in grayordinates >>>>> 43,50,50 ---> 2nd entry in grayordinates >>>>> etc. >>>>> >>>>> This is more rigorous than, for instance, saying the grayordinates >>>>> start >>>>> from somewhere in the left cortex. The translation map would help a >>>>>lot >>>>> when CIFTI data are analyzed as you suggested in your reply. >>>>> >>>>> I hope this is not a big bother. >>>>> >>>>> thanks again, >>>>> >>>>> Alpay Özcan, D.Sc. >>>>> Research Assistant Professor >>>>> Arlington Innovation Center: >>>>> Health Research >>>>> Virginia Polytechnic Institute >>>>> and State University >>>>> 900 N. Glebe Road >>>>> Arlington VA, 22203, USA >>>>> >>>>> Tel: (571) 858-3204 >>>>> http://aic.ncr.vt.edu/~alpay >>>>> >>>>>> On 27-Mar-15 11:54, Glasser, Matthew wrote: >>>>>> The whole point of grayordinates is not to work in MNI volume space, >>>>>> but >>>>>> to work in a combined cortical surface and subcortical volume space >>>>>> with >>>>>> better grayordiante-wise correspondence across subjects. The >>>>>> improvements >>>>>> gained with grayordinates are simply not possible to achieve in MNI >>>>>> volume >>>>>> space (for sheet-like cortical regions) because of the differences >>>>>>in >>>>>> geometry between a sheetlike structure and a globular nucleus and >>>>>>the >>>>>> fact >>>>>> that people simply don¹t have topologically corresponding folding >>>>>> patterns >>>>>> over most of the brain and areas are not always on the same places >>>>>>on >>>>>> folds. >>>>>> >>>>>> If your analysis does not require explicit spatial neighborhood >>>>>> information (most kinds of analysis do not require this) you can >>>>>> simply >>>>>> analyze the CIFTI data as a matrix (which you can convert to and >>>>>>from >>>>>> CIFTI and other formats like NIFTI using wb_command -cifti-convert). >>>>>> For >>>>>> example, one can run FSL¹s melodic tool (which does not support >>>>>>CIFTI >>>>>> but >>>>>> also does not care about spatial neighborhood relationships) by >>>>>> converting >>>>>> the CIFTI data to NIFTI, running melodic, and then converting the >>>>>> results >>>>>> from NIFTI back to CIFTI. If you do require explicit spatial >>>>>> neighborhood >>>>>> information, have a look at the commands available in wb_command >>>>>>that >>>>>> work >>>>>> natively on CIFTI files (e.g. finding clusters, smoothing, >>>>>>gradients, >>>>>> etc.), or write your own (you will need to interpret the surface >>>>>> topology >>>>>> of the 32k standard meshes). >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>>> On 3/27/15, 10:42 AM, "Alpay Özcan" <[email protected]> wrote: >>>>>>> >>>>>>> Hello, >>>>>>> There is a need for understanding where exactly grayordinates >>>>>>> locations >>>>>>> are placed. The descriptions in the Neuroimage 80 papers (Glasser >>>>>>>et. >>>>>>> al) are nice and helpful but for computational purposes an >>>>>>>analytical >>>>>>> definition is necessary. My search for such definition of the >>>>>>> grayordinates did not yield much. >>>>>>> >>>>>>> With my apologies in advance if the solution already exists, would >>>>>>>it >>>>>>> be >>>>>>> possible to generate a coordinate volume cube (or 3D matrix) in the >>>>>>> MNI >>>>>>> space 91x109x91 where the voxel with the 1st grayordinates will >>>>>>> have a >>>>>>> value of 1, 2nd grayordinates have a value 2, 3rd 3 etc. and the >>>>>>> non-grayordinate voxels will have 0 values? >>>>>>> >>>>>>> An accessible format (raw, NIFTI) would also be extremely helpful. >>>>>>> >>>>>>> If there is already a solution, pointers will be appreciated. >>>>>>> >>>>>>> Thanks in advance for your help. >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> -- >>>>>>> Alpay Özcan, D.Sc. >>>>>>> Research Assistant Professor >>>>>>> Arlington Innovation Center: >>>>>>> Health Research >>>>>>> Virginia Polytechnic Institute >>>>>>> and State University >>>>>>> 900 N. Glebe Road >>>>>>> Arlington VA, 22203, USA >>>>>>> >>>>>>> Tel: (571) 858-3204 >>>>>>> http://aic.ncr.vt.edu/~alpay >>>>>>> _______________________________________________ >>>>>>> HCP-Users mailing list >>>>>>> [email protected] >>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> >>>>>> >>>>>> ________________________________ >>>>>> 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. >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> >>>> ________________________________ >>>> 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. >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> [email protected] >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ________________________________ >> 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. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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