Sorry ... I should have said 20 vertices difference.
On Tue, Nov 20, 2018 at 3:52 PM Reza Rajimehr <rajim...@gmail.com> wrote: > ... 29716 indices in RH and 29696 indices in LH of cifti file. > > > On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr <rajim...@gmail.com> wrote: > >> But there are 10 more vertices in right hemisphere than left hemisphere >> ... >> >> >> On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> Left and right are registered. >>> >>> Matt. >>> >>> From: Reza Rajimehr <rajim...@gmail.com> >>> Date: Tuesday, November 20, 2018 at 2:04 AM >>> To: Matt Glasser <glass...@wustl.edu> >>> Cc: Timothy Coalson <tsc...@mst.edu>, hcp-users < >>> 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> >>> 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> on behalf of Timothy >>>> Coalson <tsc...@mst.edu> >>>> Date: Monday, November 19, 2018 at 2:57 PM >>>> To: Reza Rajimehr <rajim...@gmail.com> >>>> Cc: hcp-users <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> >>>> 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. 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. 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