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. 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 >>> 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. 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. 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 >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
