Unfortunately there is no good way to do that as after imaging data are averaged across subjects and smoothed in MNI space, it is very hard to know from which cortical areas that mask represents. Have a look at this publication for more details:
http://www.pnas.org/content/early/2018/06/19/1801582115.short Matt. From: Aslan Satary Dizaji <[email protected]<mailto:[email protected]>> Date: Wednesday, July 18, 2018 at 8:32 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Mohammad Reza Khodaei <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact) Dear Matt, Thank you very much for your response. So if we have a mask in the MNI space which we want to apply to the rsfMRI data, what can we do without having the coordinates of surface time-series? I mean, how we can infer the map from mask to the rsfMRI data. Best regards, Aslan On Wed, Jul 18, 2018 at 5:46 PM Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: 1. rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii 2-3. 100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii Note that the surface coordinates or only valid for single individuals. There is no “standard space” (like MNI space) that properly lines up the cortical areas, instead surface registration brings the data onto a standard 32k mesh where vertex 1000 has the same neuroanatomical location across subjects. You probably don’t actually need the surface coordinates for your analysis unless you are doing something unusual. Peace, Matt. From: Aslan Satary Dizaji <[email protected]<mailto:[email protected]>> Date: Wednesday, July 18, 2018 at 12:57 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Mohammad Reza Khodaei <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact) Dear Matt, Thank you for your email. In "Resting State fMRI FIX-Denoised (Compact)" of 100 unrelated subjects, inside folder "${StudyFolder}/${Subject}/MNINonLinear", there is only one folder, "Results", which inside it there are four folders "rfMRI_REST1_LR", "rfMRI_REST1_RL", "rfMRI_REST2_LR", "rfMRI_REST2_RL". And finally inside each one of these folders, there are two "*.dtseries.nii" files and two "*.dtscalar.nii" files. So basically, in "Resting State fMRI FIX-Denoised (Compact)" of 100 unrelated subjects, there is not any folder with the name of "fsaverage_LR32k". However, I checked the other data-sets of 100 unrelated subjects, and I found that "Structural Preprocessed" of 100 unrelated subjects has the "fsaverage_LR32k" folder with the files that you mentioned. So my question is that, do we need to download this data-set too so to be able to get the coordinates of surface time-series? Also, I have three other questions: 1) Which one of these "*.dtseries.nii" files do you recommend that we use: rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii 2) For example, for subject 100307 and for left hemisphere, which one of these three "*.surf.gii" files do you recommend that we use: 100307.L.inflated.32k_fs_LR.surf.gii 100307.L.midthickness.32k_fs_LR.surf.gii 100307.L.very_inflated.32k_fs_LR.surf.gii 3) I assume that with "rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii", we should use one of the three above "*.surf.gii" files and with "rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii", we should use one of the three below "*.surf.gii" files: 100307.L.inflated_MSMAll.32k_fs_LR.surf.gii 100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii 100307.L.very_inflated_MSMAll.32k_fs_LR.surf.gii Am I right? Many many thanks in advance for your time and consideration. Best regards, Aslan ________________________________ 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
