Medial wall could have been excluded from a connectivity CIFTI file, not in the file itself, but during an operation on the file using an option like -exclude-medial-wall in the command. But I totally understand the rationale for removing it in the first place.
On Tue, Nov 20, 2018 at 12:28 AM Timothy Coalson <tsc...@mst.edu> wrote: > External interoperation with GIFTI and NIFTI data is the purpose of the > -cifti-separate command, it is much simpler than using > -cifti-export-dense-mapping. > > A central goal of CIFTI was the exclusion of non-interesting locations > from the file (this becomes more important with dense connectivity files, > and is a far larger effect for voxel structures (avoiding filling out the > entire FOV)). We do not expect people to use the > -cifti-export-dense-mapping command just for file format interoperability > (but only for special circumstances, basically if spatial relationship > information must be obtained in software without full cifti support, > without leaving the cifti format). > > Tim > > > On Mon, Nov 19, 2018 at 2:43 PM Reza Rajimehr <rajim...@gmail.com> wrote: > >> Thanks! The file that we looked into was an MSMSulc file. I guess that >> the difference of 10 indices/vertices between left and right hemis exists >> for an MSMAll file as well, but I haven’t checked it yet. >> >> One comment: The medial wall has been left out in CIFTI files because the >> medial wall is not cortical grey matter. This is legitimate, however, it >> introduces confusions when communicating between CIFTI and GIFTI files. It >> would be nice if HCP developers, in future, consider a version of CIFTI >> with medial wall included. >> >> >> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson <tsc...@mst.edu> wrote: >> >>> The left and right hemisphere are intended to be in register, though I >>> don't recall what effort was put into this in MSMAll (maybe only the >>> dedrifting to sulc). I believe the left and right hemisphere medial wall >>> masks were generated separately without trying to synchronize across >>> hemispheres, and used early on, and for ongoing compatibility we stayed >>> with the same masks. >>> >>> Tim >>> >>> >>> On Mon, Nov 19, 2018 at 11:51 AM Reza Rajimehr <rajim...@gmail.com> >>> wrote: >>> >>>> We successfully used -cifti-export-dense-mapping to get the mapping >>>> from cifti indices to surface vertices (all indices are zero-based). >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT >>>> leftcortex.txt >>>> >>>> wb_command -cifti-export-dense-mapping >>>> 100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_RIGHT >>>> rightcortex.txt >>>> >>>> In the text files, there are 29696 left hemisphere indices and 29716 >>>> right hemisphere indices. I always thought that left and right hemispheres >>>> are in register in the standard space/mesh, and I was expecting to see the >>>> same number of indices/vertices (exactly 29706) for both hemispheres. But >>>> apparently this is not the case! Any reason for this? >>>> >>>> >>>> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson <tsc...@mst.edu> >>>> wrote: >>>> >>>>> The easiest to use (especially if your goal is to match other cifti >>>>> files) is generally -cifti-create-dense-from-template. It will even turn >>>>> a >>>>> 59k surface-only cifti into a standard 91282 cifti (or vice versa, if you >>>>> are so inclined). >>>>> >>>>> Yes, -cifti-export-dense-mapping will give you the cifti index to >>>>> gifti vertex mapping as a text file, if you want to do things the hard >>>>> way. >>>>> >>>>> Tim >>>>> >>>>> >>>>> On Fri, Nov 16, 2018 at 2:06 PM Harms, Michael <mha...@wustl.edu> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> See the various -cifti-create-* commands. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Michael Harms, Ph.D. >>>>>> >>>>>> ----------------------------------------------------------- >>>>>> >>>>>> Associate Professor of Psychiatry >>>>>> >>>>>> Washington University School of Medicine >>>>>> >>>>>> Department of Psychiatry, Box 8134 >>>>>> >>>>>> 660 South Euclid Ave >>>>>> <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. >>>>>> Tel: 314-747-6173 >>>>>> >>>>>> St. Louis, MO 63110 Email: mha...@wustl.edu >>>>>> >>>>>> >>>>>> >>>>>> *From: *Reza Rajimehr <rajim...@gmail.com> >>>>>> *Date: *Friday, November 16, 2018 at 1:50 PM >>>>>> *To: *"Harms, Michael" <mha...@wustl.edu> >>>>>> *Cc: *"Glasser, Matthew" <glass...@wustl.edu>, " >>>>>> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>>> *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and >>>>>> gifti files >>>>>> >>>>>> >>>>>> >>>>>> Is there a command to convert LH (or RH) gifti file to hcp cifti file? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Nov 16, 2018 at 10:55 PM Harms, Michael <mha...@wustl.edu> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> No, it is more complicated than that. >>>>>> >>>>>> >>>>>> >>>>>> I believe what you need is -cifti-export-dense-mapping >>>>>> >>>>>> >>>>>> >>>>>> Cheers, >>>>>> >>>>>> -MH >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Michael Harms, Ph.D. >>>>>> >>>>>> ----------------------------------------------------------- >>>>>> >>>>>> Associate Professor of Psychiatry >>>>>> >>>>>> Washington University School of Medicine >>>>>> >>>>>> Department of Psychiatry, Box 8134 >>>>>> >>>>>> 660 South Euclid Ave >>>>>> <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. >>>>>> Tel: 314-747-6173 >>>>>> >>>>>> St. Louis, MO 63110 Email: mha...@wustl.edu >>>>>> >>>>>> >>>>>> >>>>>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Reza >>>>>> Rajimehr <rajim...@gmail.com> >>>>>> *Date: *Friday, November 16, 2018 at 1:17 PM >>>>>> *To: *"Glasser, Matthew" <glass...@wustl.edu> >>>>>> *Cc: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>>> *Subject: *Re: [HCP-Users] Number of cortical vertices in cifti and >>>>>> gifti files >>>>>> >>>>>> >>>>>> >>>>>> Thanks! Can I simply say that: >>>>>> >>>>>> >>>>>> >>>>>> For left hemisphere: >>>>>> >>>>>> vertex number in cifti = vertex number (up to 29706) in LH gifti >>>>>> >>>>>> >>>>>> >>>>>> For right hemisphere: >>>>>> >>>>>> vertex number in cifti = vertex number (up to 29706) in RH gifti + >>>>>> 29706 >>>>>> >>>>>> >>>>>> >>>>>> Or the mapping is more complicated than this? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Nov 16, 2018 at 9:56 PM Glasser, Matthew <glass...@wustl.edu> >>>>>> wrote: >>>>>> >>>>>> That is correct, the medial wall is kept out. Usually when I want to >>>>>> do that I split the CIFTI file into hemispheric GIFTI files, but perhaps >>>>>> there is a good way to load in a specific mapping based on something we >>>>>> can >>>>>> output from wb_command. >>>>>> >>>>>> >>>>>> >>>>>> Matt. >>>>>> >>>>>> >>>>>> >>>>>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Reza >>>>>> Rajimehr <rajim...@gmail.com> >>>>>> *Date: *Friday, November 16, 2018 at 10:17 AM >>>>>> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>>> *Subject: *[HCP-Users] Number of cortical vertices in cifti and >>>>>> gifti files >>>>>> >>>>>> >>>>>> >>>>>> Hi, >>>>>> >>>>>> >>>>>> >>>>>> A cifti file has 91282 vertices/voxels, a combined LR cifti file has >>>>>> 59412 vertices, and an individual hemisphere gifti file has 32492 >>>>>> vertices. >>>>>> So the number of cortical vertices in cifti files is less than the number >>>>>> of cortical vertices in gifti files (left hemi vertices + right hemi >>>>>> vertices = 64984). Looks like this is related to not having medial wall >>>>>> vertices in the cifti files, right? >>>>>> >>>>>> >>>>>> >>>>>> We have loaded these files in Matlab. Now we want to know which >>>>>> vertex in right (or left) hemisphere gifti file corresponds to which >>>>>> vertex >>>>>> in the cifti file. How can we achieve this? >>>>>> >>>>>> >>>>>> >>>>>> Best, >>>>>> >>>>>> Reza >>>>>> >>>>>> _______________________________________________ >>>>>> HCP-Users mailing list >>>>>> HCP-Users@humanconnectome.org >>>>>> 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. 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