I'm not entirely sure how to get .label.gii files translated to freesurfer .annot format, and a question on exactly this on the freesurfer list went unanswered. I think we have done this before, but the details I am aware of suggest that "mris_convert --annot" should behave reasonably (given that the colors are unique, which I believe they are for the HCP MMP v1.0). Does "mris_convert --annot" work for you, and if not, what is the error?
If you want to get something like the average timeseries within each label, you could instead try option B of FAQ 9 to take your surface data the other direction to fs_LR, create a cifti file from it with -cifti-create-dense-from-template or -cifti-create-dense-timeseries, then use the -cifti-parcellate command (and since the MMP v1.0 doesn't have subcortical definitions, you could ignore the subcortical data for now). Tim On Thu, Sep 8, 2016 at 9:48 AM, Khadka, Sabin <sabin.kha...@hhchealth.org> wrote: > 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-bounces@ > 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] > *Sent:* Thursday, August 18, 2016 6:01 PM > *To:* Khadka, Sabin; 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> on behalf of "Khadka, > Sabin" <sabin.kha...@hhchealth.org> > *Date: *Thursday, August 18, 2016 at 2:41 PM > *To: *"hcp-users@humanconnectome.org" <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. If you are not the intended recipient, or an employee or agent > responsible for delivering the message to the intended recipient, please > contact the sender by reply e-mail and destroy all copies of the original > message, including any attachments. * > > _______________________________________________ > 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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