Dear HCP-Freesurfers, I'd like to extract the mean cortical thickness of a ROI I generated for subjects from the human connectome project (HCP). The ROI is a mask in nifti format and its dimensions correspond to the HCP_subject/MNINonLinear/T1w_restore_brain.nii.gz file. I'd like to use the normalized, structural HCP data from the preprocessed Freesurfer pipeline. Trying to follow the instruction on the Freesurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), I encountered several problems. I hope you can help me!
How do I map the subject thickness data to the fsaverage subject? There are several "thickness" files in the HCP dataset - which one should be used? I created a "surf" folder and filled it with the supposedly relevant files. Is the used file for the --surfreg flag correct (see command line below)? I tried to use the following command: mri_surf2surf --srcsubject 100408 --srcsurfval 100408.R.thickness.32k_fs_LR.shape.gii --trgsubject fsaverage --trgsurfval rh.checkthickness.fsaverage.mgh --hemi rh --surfreg 100408.R.sphere.reg.native.surf.gii This error message resulted: Source registration surface changed to 100408.R.sphere.reg.native.surf.gii Target registration surface changed to 100408.R.sphere.reg.native.surf.gii srcsubject = 100408 srcval = 100408.R.thickness.32k_fs_LR.shape.gii srctype = trgsubject = fsaverage trgval = rh.checkthickness.fsaverage.mgh trgtype = srcsurfreg = 100408.R.sphere.reg.native.surf.gii trgsurfreg = 100408.R.sphere.reg.native.surf.gii srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usr/local/freesurfer/subjects/100408/surf/rh.100408.R.sphere.reg.native.surf.gii Loading source data ** failed to open GIFTI XML file '/usr/local/freesurfer/subjects/100408/surf/100408.R.thickness.32k_fs_LR.shape.gii' MRISreadGiftiAsMRI: gifti_read_image() returned NULL ERROR: could not read 100408.R.thickness.32k_fs_LR.shape.gii as type 27 I appreciate your help. Cheers, Jessica _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
