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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-bounces@nmr.mgh.harvard.edu on behalf of "Ni, Zhen (NIH/NINDS) [C]" zhen.ni@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
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