Re: [HCP-Users] creati cifti from nifti1

[Glasser, Matthew]

The medial wall ROIs are ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii. Peace, Matt. From: Timothy Coalson <tsc...@mst.edu> Date: Friday, February 27, 2015 at 6:44 PM To: Marta Moreno <mmorenoort...@icloud.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] creati cifti from nifti1 We are going to need a bit more information than that, I don't know what you mean by "subcortical data is not separated from the surface", do you mean that the cortex data is represented in voxels in the cifti file also? You should be using the -left-metric and -right-metric options for the surface data (and -roi-left and -roi-right options to exclude the medial wall), and -volume with a label volume that has only the subcortical labels of interest in it, that is, it should not have CORTEX_LEFT and CORTEX_RIGHT labels (unless you want the cortex data to be represented as voxels also). If you want to do comparisons between it and the HCP released data, you'll likely want to use the medial wall rois and label volume that we use for our grayordinate space, rather than files derived from the subject.  The surface ROIs can be retrieved from an existing HCP cifti file with -cifti-separate using the -metric and -roi options.  The volume label file exists in HCP subject directories (I don't know if it exists somewhere else also), here: ${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz Tim On Fri, Feb 27, 2015 at 5:53 PM, Marta Moreno <mmorenoort...@icloud.com> wrote: Hi users, I am working on 7 T data doing some testing for fc analyses and would like to to create a cifti file from nifti1 (my nifti1 fc t-map was created with SPM).  I am using wb_command -volume-to-surface-mapping and wb_command -cifti-create-dense-scalar to have my cifti file but when loading into workbench my subcortical data is not separated from my surface t-map.  What am I doing wrong? Thanks, Leah _______________ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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. 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users