Thanks Tim and Matthew! Tim's answer is what I needed, I missed these two commands. I tried them and got the area size and volume successfully just now.
The analysis I used is to measure the area size of each ROIs (ROI comes from different parcellations), and measure which region have larger area size. The reason I did this is because the area size is different from vertex number (e.g. regions with the same vertex number, or they looked similar do not mean they have same area size, while their area size may varied a lot). I think it is important for measuring or describing the property of a region. However, many published paper does not list this information. One more question to Tim, do you mean the better way to compare area sizes between subjects is in subject-specific space but not the standard space (e.g. fsLR_32k)? Due to many atlases had been aligned to the standard space, I guess the area size in the standard space is representative, but I don't know the bias when measuring area size in the standard space. Best, Taicheng On 2/24/2019 02:00，<hcp-users-requ...@humanconnectome.org> wrote： Send HCP-Users mailing list submissions to hcp-users@humanconnectome.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.humanconnectome.org/mailman/listinfo/hcp-users or, via email, send a message with subject or body 'help' to hcp-users-requ...@humanconnectome.org You can reach the person managing the list at hcp-users-ow...@humanconnectome.org When replying, please edit your Subject line so it is more specific than "Re: Contents of HCP-Users digest..." Today's Topics: 1. Confusion about Destrieux labels (Reza Rajimehr) 2. Re: Confusion about Destrieux labels (Timothy Coalson) 3. Surface area size of fsLR space (Huang Taicheng) 4. Re: Surface area size of fsLR space (Glasser, Matthew) 5. Re: Surface area size of fsLR space (Timothy Coalson) 6. Re: Confusion about Destrieux labels (Reza Rajimehr) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Feb 2019 18:08:07 +0000 From: Reza Rajimehr <rajim...@gmail.com> Subject: [HCP-Users] Confusion about Destrieux labels To: hcp-users <hcp-users@humanconnectome.org> Message-ID: <CAPiNLe4=XGA0WTFH=hlu2f2m70qej73a0cqxrs2l7umyupx...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, We have loaded Destrieux parcellation of one of the HCP subjects (100206.L.aparc.a2009s.32k_fs_LR.label.gii) in Matlab. It includes 76 labels. Label 1 is ??? and label 2 is G_and_S_frontomargin. However, Destrieux paper describes 74 labels and their label 1 is G_and_S_frontomargin. Could you please explain this discrepancy? Thanks, Reza -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20190222/a1893742/attachment-0001.html ------------------------------ Message: 2 Date: Fri, 22 Feb 2019 17:59:23 -0600 From: Timothy Coalson <tsc...@mst.edu> Subject: Re: [HCP-Users] Confusion about Destrieux labels To: Reza Rajimehr <rajim...@gmail.com> Cc: hcp-users <hcp-users@humanconnectome.org> Message-ID: <CAK_=taz4fapwxtodrwa9kacbxjcbliob1d99x2pvbjjm7lq...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" In that gifti file, the label table indicates that ??? is label 0, as is recommended (it means things that haven't been labeled, such as the medial wall). The matlab gifti library must be shifting these values, possibly because they are taken as indices into another matlab array (matlab doesn't accept 0 as an array index). However, the labels appear to go up to 75 (L_S_temporal_transverse) in the gifti file. I would expect that the freesurfer outputs already contain 75 labels. Tim On Fri, Feb 22, 2019 at 12:08 PM Reza Rajimehr <rajim...@gmail.com> wrote: Hi, We have loaded Destrieux parcellation of one of the HCP subjects (100206.L.aparc.a2009s.32k_fs_LR.label.gii) in Matlab. It includes 76 labels. Label 1 is ??? and label 2 is G_and_S_frontomargin. However, Destrieux paper describes 74 labels and their label 1 is G_and_S_frontomargin. Could you please explain this discrepancy? Thanks, Reza _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20190222/0825fb01/attachment-0001.html ------------------------------ Message: 3 Date: Sat, 23 Feb 2019 10:29:23 +0800 (GMT+08:00) From: "Huang Taicheng" <hitech9...@gmail.com> Subject: [HCP-Users] Surface area size of fsLR space To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Message-ID: <7dae9f4a.90b9.169182f8e13.coremail.hitech9...@gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I'm trying to convert vertex number to area size in fsLR space because area size, rather than vertex number, is comparable across data from different coordinate space (e.g. fsaverage, fsLR). However, unlike to freesurfer, I could not find any files like lh.area in HCP folders. This paper (see reference) mentioned that all of the gray matter sampled at a 2 mm average vertex spacing on the surface and as 2 mm voxels subcortically. Could I explain this as the area size of each vertex is 4 mm2, and they are isotropic? I have calculated if my understanding is right, the volume of the grey matter in left hemisphere is 259936 mm3, which is similar to the value calculated in fsaverage space (by checking information of aseg.stats, 277114.15 mm3 as one of my subject). I could not make sure if my understanding is correct, more information is better for me to do further analysis. Thanks in advance! Taicheng Reference: Glasser MF, et al. (2013) The minimal preprocessing pipelines for the human connectome project. Neuroimage 80:105-124. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20190223/021bfc2b/attachment-0001.html ------------------------------ Message: 4 Date: Sat, 23 Feb 2019 02:44:52 +0000 From: "Glasser, Matthew" <glass...@wustl.edu> Subject: Re: [HCP-Users] Surface area size of fsLR space To: Huang Taicheng <hitech9...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Message-ID: <d8960f95.18d2e4%glass...@wustl.edu> Content-Type: text/plain; charset="us-ascii" Some more details on why you want to do this would be helpful to provide the most useful response. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Huang Taicheng <hitech9...@gmail.com<mailto:hitech9...@gmail.com>> Date: Friday, February 22, 2019 at 8:29 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Surface area size of fsLR space Hello, I'm trying to convert vertex number to area size in fsLR space because area size, rather than vertex number, is comparable across data from different coordinate space (e.g. fsaverage, fsLR). However, unlike to freesurfer, I could not find any files like lh.area in HCP folders. This paper (see reference) mentioned that all of the gray matter sampled at a 2 mm average vertex spacing on the surface and as 2 mm voxels subcortically. Could I explain this as the area size of each vertex is 4 mm2, and they are isotropic? I have calculated if my understanding is right, the volume of the grey matter in left hemisphere is 259936 mm3, which is similar to the value calculated in fsaverage space (by checking information of aseg.stats, 277114.15 mm3 as one of my subject). I could not make sure if my understanding is correct, more information is better for me to do further analysis. Thanks in advance! Taicheng Reference: Glasser MF, et al. (2013) The minimal preprocessing pipelines for the human connectome project. Neuroimage 80:105-124. _______________________________________________ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20190223/3cb37e90/attachment-0001.html ------------------------------ Message: 5 Date: Fri, 22 Feb 2019 21:13:27 -0600 From: Timothy Coalson <tsc...@mst.edu> Subject: Re: [HCP-Users] Surface area size of fsLR space To: Huang Taicheng <hitech9...@gmail.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Message-ID: <CAK_=tawk7vmxboxruv+px+e9uhaenfhsgr_58axpcokrcwo...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" The command wb_command -surface-vertex-areas will give you the area of each vertex. For vertex volume, you should use wb_command -surface-wedge-volume. When comparing these kinds of measures, it is usually better to measure them in an anatomically faithful space (such as the T1w space of each subject, which is only rigidly registered). Tim On Fri, Feb 22, 2019 at 8:29 PM Huang Taicheng <hitech9...@gmail.com> wrote: Hello, I'm trying to convert vertex number to area size in fsLR space because area size, rather than vertex number, is comparable across data from different coordinate space (e.g. fsaverage, fsLR). However, unlike to freesurfer, I could not find any files like lh.area in HCP folders. This paper (see reference) mentioned that all of the gray matter sampled at a 2 mm average vertex spacing on the surface and as 2 mm voxels subcortically. Could I explain this as the area size of each vertex is 4 mm2, and they are isotropic? I have calculated if my understanding is right, the volume of the grey matter in left hemisphere is 259936 mm3, which is similar to the value calculated in fsaverage space (by checking information of aseg.stats, 277114.15 mm3 as one of my subject). I could not make sure if my understanding is correct, more information is better for me to do further analysis. Thanks in advance! Taicheng Reference: Glasser MF, et al. (2013) The minimal preprocessing pipelines for the human connectome project. Neuroimage 80:105-124. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20190222/3268478a/attachment-0001.html ------------------------------ Message: 6 Date: Sat, 23 Feb 2019 15:45:07 +0000 From: Reza Rajimehr <rajim...@gmail.com> Subject: Re: [HCP-Users] Confusion about Destrieux labels To: Timothy Coalson <tsc...@mst.edu>, hcp-users <hcp-users@humanconnectome.org> Message-ID: <CAPiNLe5VvyQeE=yurZZD4=dd8admyt13ka+hg1dxp8dnbfb...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Thanks Tim! One remaining issue: no vertices has the label code 42 (Lat_Fis-post). I guess this is inherited from Freesurfer? On Fri, Feb 22, 2019 at 11:59 PM Timothy Coalson <tsc...@mst.edu> wrote: In that gifti file, the label table indicates that ??? is label 0, as is recommended (it means things that haven't been labeled, such as the medial wall). The matlab gifti library must be shifting these values, possibly because they are taken as indices into another matlab array (matlab doesn't accept 0 as an array index). However, the labels appear to go up to 75 (L_S_temporal_transverse) in the gifti file. I would expect that the freesurfer outputs already contain 75 labels. Tim On Fri, Feb 22, 2019 at 12:08 PM Reza Rajimehr <rajim...@gmail.com> wrote: Hi, We have loaded Destrieux parcellation of one of the HCP subjects (100206.L.aparc.a2009s.32k_fs_LR.label.gii) in Matlab. It includes 76 labels. Label 1 is ??? and label 2 is G_and_S_frontomargin. However, Destrieux paper describes 74 labels and their label 1 is G_and_S_frontomargin. Could you please explain this discrepancy? Thanks, Reza _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -------------- next part -------------- An HTML attachment was scrubbed... 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