[Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas
Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas
Hi Daniel, have you run recon-all on your subjects? If so, you can run mri_annotation2label to convert the ?h.aparc.annot file into separate labels for each ROI, then go from there. Or if you want to do everything in average space you can run it on fsaverage (or load the annotation in tksurfer, click on the one you want and save it as a label instead of converting every parcel to a label) cheers Bruce On Wed, 19 Jun 2013, Yang, Daniel wrote: Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas
If you want to use it as a mask in FSFAST, you can do that at the higher level when you run mri_glmfit. You would then extract the label for fsaverage only and pass it to mri_glmfit with the --label option doug On 6/19/13 11:22 AM, Bruce Fischl wrote: Hi Daniel, have you run recon-all on your subjects? If so, you can run mri_annotation2label to convert the ?h.aparc.annot file into separate labels for each ROI, then go from there. Or if you want to do everything in average space you can run it on fsaverage (or load the annotation in tksurfer, click on the one you want and save it as a label instead of converting every parcel to a label) cheers Bruce On Wed, 19 Jun 2013, Yang, Daniel wrote: Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
