Re: [HCP-Users] Questions regarding coordinates infomation of vertex
I am now trying to get mapping matrix from *.sur.gii using nibabel. I have to say it's not easy to find that matrix, hiding so deep in the file. Thank you for your reminding! I am very very grateful! Qinqin lee On 03/20/2017 23:05，Timothy Coalson<tsc...@mst.edu> wrote： Also note that cifti files can contain both left and right hemispheres and voxel data, while gifti files, including *.surf.gii, only contain one hemisphere per file. There is some explanation here: http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-help Note that cifti files generally exclude the medial wall from being represented in the matrix, such that there are 29k indices that represent the left cortex in our standard cifti space, but the left cortex surface has 32k vertices. Nibabel has some very new support for reading cifti files in python, which should give the information of what each index in the cifti file means (specifically which vertex index or voxel each spatial index represents - the vertex coordinates are not in cifti files, so you need to get coordinates from *.surf.gii files). You may need to grab the latest version from github: https://github.com/nipy/nibabel Tim On Mon, Mar 20, 2017 at 8:39 AM, Irisqql0922 <irisqql0...@163.com> wrote: Sorry, I thought Matt misunderstanding my words. Ok, I will check the file *midthickness*.sur.gii. Thank you Donna, and thank you Matt^_^ Qinqin Lee On 03/20/2017 21:25，Dierker, Donna<do...@wustl.edu> wrote： Hi Qinqin, As Matt said, the file named like *midthickness*.surf.gii contains the vertex-to-3D coordinate mapping that you seek. This could be an individual’s surface, if the cifti data pertains to a particular subject, or it could be a mean midthickness (e.g., HCP500) if it is group data. You can read about the GIFTI file format here: https://www.nitrc.org/projects/gifti/ Also, have a look here and consider whether this command might help: https://www.humanconnectome.org/documentation/workbench-command/command-all-commands-help.html -cifti-rois-from-extrema You might have to manipulate your ROI to narrow it down first. Donna > On Mar 20, 2017, at 7:23 AM, Irisqql0922 <irisqql0...@163.com> wrote: > > > Thank you Glasser, but your answer is not what I'm looking for. I may not > express myself clearly. > Here is the situation: I am trying to analysis CIFTI data using python. Now > I have got a matrix with all threshold vertex value. Next, I want to use > that matrix to generate a mask for my future analysis . But now, what I got > is just a matrix with only vertex values , thus I cannot use this matrix to > generate my ROIs and then get their spatial coordinates. > So I wonder if there is a transformation matrix to transform vertex index to > spatial coordinates, and if there is, where can I find it. > > Thanks again, > Qinqin lee > > On 03/20/2017 20:03，Glasser, Matthew<glass...@wustl.edu> wrote： > In individual subjects, you can use the midthickness surface coordinates as > the 3D coordinates. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Irisqql0922 > <irisqql0...@163.com> > Date: Monday, March 20, 2017 at 4:19 AM > To: hcp-users <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Questions regarding coordinates infomation of vertex > > Dear HCP teams, > > I am trying to threshold surface data of file *.dscalar.nii , and after that, > I don't know how to link data remains in the matrix with its space > coordinates. Is there any matrix contains the information linking vertex > index in the matrix with its space location? If there is such a matrix, where > can I find it? > > Regards, > Qinqin lee > > > ___ > 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 advise
Re: [HCP-Users] Questions regarding coordinates infomation of vertex
Hi Qinqin, As Matt said, the file named like *midthickness*.surf.gii contains the vertex-to-3D coordinate mapping that you seek. This could be an individual’s surface, if the cifti data pertains to a particular subject, or it could be a mean midthickness (e.g., HCP500) if it is group data. You can read about the GIFTI file format here: https://www.nitrc.org/projects/gifti/ Also, have a look here and consider whether this command might help: https://www.humanconnectome.org/documentation/workbench-command/command-all-commands-help.html -cifti-rois-from-extrema You might have to manipulate your ROI to narrow it down first. Donna > On Mar 20, 2017, at 7:23 AM, Irisqql0922 <irisqql0...@163.com> wrote: > > > Thank you Glasser, but your answer is not what I'm looking for. I may not > express myself clearly. > Here is the situation: I am trying to analysis CIFTI data using python. Now > I have got a matrix with all threshold vertex value. Next, I want to use > that matrix to generate a mask for my future analysis . But now, what I got > is just a matrix with only vertex values , thus I cannot use this matrix to > generate my ROIs and then get their spatial coordinates. > So I wonder if there is a transformation matrix to transform vertex index to > spatial coordinates, and if there is, where can I find it. > > Thanks again, > Qinqin lee > > On 03/20/2017 20:03，Glasser, Matthew<glass...@wustl.edu> wrote： > In individual subjects, you can use the midthickness surface coordinates as > the 3D coordinates. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Irisqql0922 > <irisqql0...@163.com> > Date: Monday, March 20, 2017 at 4:19 AM > To: hcp-users <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Questions regarding coordinates infomation of vertex > > Dear HCP teams, > > I am trying to threshold surface data of file *.dscalar.nii , and after that, > I don't know how to link data remains in the matrix with its space > coordinates. Is there any matrix contains the information linking vertex > index in the matrix with its space location? If there is such a matrix, where > can I find it? > > Regards, > Qinqin lee > > > ___ > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Questions regarding coordinates infomation of vertex
Thank you Glasser, but your answer is not what I'm looking for. I may not express myself clearly. Here is the situation: I am trying to analysis CIFTI data using python. Now I have got a matrix with all threshold vertex value. Next, I want to use that matrix to generate a mask for my future analysis . But now, what I got is just a matrix with only vertex values , thus I cannot use this matrix to generate my ROIs and then get their spatial coordinates. So I wonder if there is a transformation matrix to transform vertex index to spatial coordinates, and if there is, where can I find it. Thanks again, Qinqin lee On 03/20/2017 20:03，Glasser, Matthew<glass...@wustl.edu> wrote： In individual subjects, you can use the midthickness surface coordinates as the 3D coordinates. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Irisqql0922 <irisqql0...@163.com> Date: Monday, March 20, 2017 at 4:19 AM To: hcp-users <hcp-users@humanconnectome.org> Subject: [HCP-Users] Questions regarding coordinates infomation of vertex Dear HCP teams, I am trying to threshold surface data of file *.dscalar.nii , and after that, I don't know how to link data remains in the matrix with its space coordinates. Is there any matrix contains the information linking vertex index in the matrix with its space location? If there is such a matrix, where can I find it? Regards, Qinqin lee ___ 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
Re: [HCP-Users] Questions regarding coordinates infomation of vertex
In individual subjects, you can use the midthickness surface coordinates as the 3D coordinates. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Irisqql0922 <irisqql0...@163.com<mailto:irisqql0...@163.com>> Date: Monday, March 20, 2017 at 4:19 AM To: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Questions regarding coordinates infomation of vertex Dear HCP teams, I am trying to threshold surface data of file *.dscalar.nii , and after that, I don't know how to link data remains in the matrix with its space coordinates. Is there any matrix contains the information linking vertex index in the matrix with its space location? If there is such a matrix, where can I find it? Regards, Qinqin lee ___ 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. 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] Questions regarding coordinates infomation of vertex
Dear HCP teams, I am trying to threshold surface data of file *.dscalar.nii , and after that, I don't know how to link data remains in the matrix with its space coordinates. Is there any matrix contains the information linking vertex index in the matrix with its space location? If there is such a matrix, where can I find it? Regards, Qinqin lee ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
