Hi- Thanks for the information on how to map data between freesurfer and HCP. I have tried few things and haven't been able to succeed in what I am trying to do. I was wondering if somebody can help me on this regard.
We are not able to use HCP pipeline to process our data because our data was not collected with similar specifications. Thus, we've used FSFAST program to process our rsfMRI data which maps data to freesurfer's fsaverage space. We can extract the roi values using the freesurfer's annotation files. No, we plan to extract these (FSFAST/freesurfer processed) data using HCP's 180 parcellation. Using the instruction (FAQ#9 option C), I 've successfully created the label files (see below for commands I've used). Now, I want to use these label files to extract roi values from my data. How can I use these output label files (FS_out.area.lh.k_fsavg.label.gii) in freesurfer space. I've tried to convert them using mris_convert but that doesn't work. wb_command -cifti-separate Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_PhaseTwo/Q1-Q6_RelatedParcellation210/MNINonLinear/fsaverage_LR32k/Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Final_Final_Areas_Group.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_LEFT try2_metric_out_left.label.gii wb_command -cifti-separate Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_PhaseTwo/Q1-Q6_RelatedParcellation210/MNINonLinear/fsaverage_LR32k/Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Final_Final_Areas_Group.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_RIGHT try2_metric_out_right.label.gii wb_command -label-resample try2_metric_out_left.label.gii standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.L.164k_fsavg_L.surf.gii ADAP_BARY_AREA FS_out.area.lh.k_fsavg.label.gii -area-metrics standard_mesh_atlases/resample_fsaverage/fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii standard_mesh_atlases/resample_fsaverage/fs_LR.L.midthickness_va_avg.164k_fs_LR.shape.gii wb_command -label-resample try2_metric_out_right.label.gii standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.R.164k_fsavg_R.surf.gii ADAP_BARY_AREA FS_out.area.rh.k_fsavg.label.gii -area-metrics standard_mesh_atlases/resample_fsaverage/fs_LR.R.midthickness_va_avg.32k_fs_LR.shape.gii standard_mesh_atlases/resample_fsaverage/fs_LR.R.midthickness_va_avg.164k_fs_LR.shape.gii Thanks for help! -Sabin From: hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Khadka, Sabin Sent: Friday, August 19, 2016 12:42 PM To: Glasser, Matthew; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] 180 parcellation for freesurfer? Hi Matt- Yes I would like to give it a try. If you could send it to me that'd great. -Sabin From: Glasser, Matthew [mailto:glass...@wustl.edu]<mailto:[mailto:glass...@wustl.edu]> Sent: Thursday, August 18, 2016 6:01 PM To: Khadka, Sabin; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] 180 parcellation for freesurfer? We've been working on an HCP WIKI "FAQ" entry on this topic and will announce it on the mailing list. If you are interested in beta testing this, let us know and we can send it to you. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Khadka, Sabin" <sabin.kha...@hhchealth.org<mailto:sabin.kha...@hhchealth.org>> Date: Thursday, August 18, 2016 at 2:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] 180 parcellation for freesurfer? Hi all- I want to use 180 parcellation from Glasser et al 2016 to extract values from subjects that are mapped into freesurfer's fsaverage space. I was wondering if that is possible and if 180 parcellation are converted into freesurfer compatible annotation format (or label files)? Thanks. This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. 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