Left and right are registered. Matt.
From: Reza Rajimehr <rajim...@gmail.com<mailto:rajim...@gmail.com>> Date: Tuesday, November 20, 2018 at 2:04 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti files Thanks Matt! Yes, having symmetric medial wall and having registered left and right hemispheres would be helpful and important. On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: We don’t want the non-greymatter medial wall in CIFTI; however, the medial wall may undergo revision in the future and making it symmetric might be more convenient, though this would might require rerunning the left/right registration, which remains in all HCP Pipelines derived standard mesh CIFTI and GIFTI files from the original landmark-based registration published in Van Essen et al 2012 Cerebral Cortex. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Monday, November 19, 2018 at 2:57 PM To: Reza Rajimehr <rajim...@gmail.com<mailto:rajim...@gmail.com>> Cc: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti files 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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:mha...@wustl.edu> From: Reza Rajimehr <rajim...@gmail.com<mailto:rajim...@gmail.com>> Date: Friday, November 16, 2018 at 1:50 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Reza Rajimehr <rajim...@gmail.com<mailto:rajim...@gmail.com>> Date: Friday, November 16, 2018 at 1:17 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Reza Rajimehr <rajim...@gmail.com<mailto:rajim...@gmail.com>> Date: Friday, November 16, 2018 at 10:17 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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. 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. 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