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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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
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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.