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Hi Varun,
I’m not sure what issue that you have been running into. Can you send your
recon-all.log?
In general, you need to
1. set environment variable SUBJECTS_DIR to some directory that you have write
permission
2. pass full path to T1 image to -i <full_path_to_T1_image>
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Varun Chandran
Sent: Wednesday, June 21, 2023 10:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Pial and White surface maps are not found
External Email - Use Caution
Hi FS experts,
It's been a few years, I used FS tools for cortical surface reconstruction.
Now, when I used the freesurfer 7.2 version to perform cortical surface
reconstruction on the T1-weighted structural MRI data, I was unable to obtain
the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light
on this issue?
command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache
thanks,
best,
Varun
--
Varun Arunachalam Chandran, PhD
Postdoctoral Research Associate,
Faculty of biology, medicine and health,
School of health sciences,
University of Manchester,
United Kingdom.
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