External Email - Use Caution 1. A 512*512*90 dataset is likely a long way from an isotropic resolution dataset of 1mm isotropic or better that works best with FreeSurfer. 2. What Connectome Workbench command were you trying to run?
Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Ni, Zhen (NIH/NINDS) [C]" <zhen...@nih.gov> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, March 18, 2025 at 5:40 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Human connectome workbench Hello, I used the command “recon-all -all -subjid $SUBJECTNAME”. There was no error for Freesurfer, but it was slow at certain time points with a lot of corrections (sometimes with large defects, our initial imaging was a 512*512*90 slices T1 axial imaging set). The outputs for this were used in HCP workbench to downsample the size of the cortical sheet. When I run the workbench script, it showed an error: While running >>>>/workbench/sub-001.L.sulc.native.shape.gii CORTEX_LEFT ERROR: NAME OF FILE: sub-002.L.sulc.native.shape.gii PATH TO FILE: >>>>/sub-002/workbench File does not exist I don’t think this is a problem with workbench but should be missing some components (cortical mesh) when the initial cortical sheet was made by Freesurfer. I wonder if you have any ideas. Thanks Zhen ________________________________ 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.
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