Hi, Cortical thickness is purely a surface-based measure, so that particular dscalar indeed doesn’t contain any volume-based grayordinates.
The task fMRI data would be one example in which volume-based grayordinates are present in the CIFTI (i.e., cerebellum and subcortical voxels) Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 5/2/18, 4:30 PM, "hcp-users-boun...@humanconnectome.org on behalf of Ho, Wilson Christopher" <hcp-users-boun...@humanconnectome.org on behalf of w...@mgh.harvard.edu> wrote: Hello experts, I’m looking at the examples for FSL’s PALM on CIFTI files (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/Examples#Example_10:_Using_CIFTI_files) and one of the processing steps is separating the volume and surface data from the CIFTI. When I run wb_command’s CIFTI-Separate, I can’t seem to separate any volume data from the dscalar file specified. For example, I run: > wb_command -cifti-separate > ../352132.corrThickness_MSMAll.32k_fs_LR.dscalar.nii COLUMN -volume-all > data_sub.nii -metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT > data_R.func.gii ...and I get the error, "ERROR: specified file and direction does not contain any volume data" If the volumes are not present in the CIFTI dscalar.nii's, is there another CIFTI file with the volume present? They don't seem to be present for the native or 164k fsaverage files, or non-MSMAll files either. Is there anywhere I could locate this volume data? Or would anyone know whether they are necessary for the PALM analysis (ie. could a sufficient analysis be done by omitting the volume aspect and using solely the extracted GIFTI surfaces?). Would appreciate some insight on what seems to be a simple misunderstanding on my end. Thank you! Wilson 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. _______________________________________________ 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
